The hostname of the Pi Zero is pi3, it was the third Pi Zero I have setup (it is a bad hostname). The default bootload address on the RPUftdi (e.g. my multi-drop RS-422 board) is '0', and I have not changed it, I keep the i2c-debug firmware on an ATmega328p board under the RPUftdi for use on my test bench, so I will just upload that same program compiled from the Pi Zero.

rsutherland@pi3:~/Samba/RPUno/i2c-debug $ uname -a
Linux pi3 4.9.41+ #1023 Tue Aug 8 15:47:12 BST 2017 armv6l GNU/Linux
rsutherland@pi3:~/Samba/RPUno/i2c-debug $ make bootload
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o main.o main.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o i2c-scan.o i2c-scan.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o i2c-cmd.o i2c-cmd.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o ../Uart/id.o ../Uart/id.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o ../lib/timers.o ../lib/timers.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o ../lib/uart.o ../lib/uart.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o ../lib/twi.o ../lib/twi.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o ../lib/rpu_mgr.o ../lib/rpu_mgr.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o ../lib/adc.o ../lib/adc.c
avr-gcc -Os -g -std=gnu99 -Wall -ffunction-sections -fdata-sections  -DF_CPU=16000000UL   -DBAUD=38400UL -I.  -mmcu=atmega328p -c -o ../lib/parse.o ../lib/parse.c
avr-gcc -Wl,-Map,I2c-debug.map  -Wl,--gc-sections  -mmcu=atmega328p main.o i2c-scan.o i2c-cmd.o ../Uart/id.o ../lib/timers.o ../lib/uart.o ../lib/twi.o ../lib/rpu_mgr.o ../lib/adc.o ../lib/parse.o -o I2c-debug.elf
avr-size -C --mcu=atmega328p I2c-debug.elf
AVR Memory Usage
----------------
Device: atmega328p
Program:    8684 bytes (26.5% Full)
(.text + .data + .bootloader)
Data:        375 bytes (18.3% Full)
(.data + .bss + .noinit)
rm -f I2c-debug.o main.o i2c-scan.o i2c-cmd.o ../Uart/id.o ../lib/timers.o ../lib/uart.o ../lib/twi.o ../lib/rpu_mgr.o ../lib/adc.o ../lib/parse.o
avr-objcopy -j .text -j .data -O ihex I2c-debug.elf I2c-debug.hex
rm -f I2c-debug.elf
avrdude -v -p atmega328p -c arduino -P /dev/ttyAMA0 -b 115200 -U flash:w:I2c-debug.hex
avrdude: Version 6.1, compiled on Jul  7 2015 at 10:29:47         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/         Copyright (c) 2007-2014 Joerg Wunsch
         System wide configuration file is "/etc/avrdude.conf"         User configuration file is "/home/rsutherland/.avrduderc"         User configuration file does not exist or is not a regular file, skipping
         Using Port                    : /dev/ttyAMA0         Using Programmer              : arduino         Overriding Baud Rate          : 115200         AVR Part                      : ATmega328P         Chip Erase delay              : 9000 us         PAGEL                         : PD7         BS2                           : PC2         RESET disposition             : dedicated         RETRY pulse                   : SCK         serial program mode           : yes         parallel program mode         : yes         Timeout                       : 200         StabDelay                     : 100         CmdexeDelay                   : 25         SyncLoops                     : 32         ByteDelay                     : 0         PollIndex                     : 3         PollValue                     : 0x53         Memory Detail                 :
                                  Block Poll               Page                       Polled           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------           eeprom        65    20     4    0 no       1024    4      0  3600  3600 0xff 0xff           flash         65     6   128    0 yes     32768  128    256  4500  4500 0xff 0xff           lfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00           hfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00           efuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00           lock           0     0     0    0 no          1    0      0  4500  4500 0x00 0x00           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00
         Programmer Type : Arduino         Description     : Arduino         Hardware Version: 3         Firmware Version: 4.4         Vtarget         : 0.3 V         Varef           : 0.3 V         Oscillator      : 28.800 kHz         SCK period      : 3.3 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.00s
avrdude: Device signature = 0x1e950f
avrdude: safemode: lfuse reads as 0
avrdude: safemode: hfuse reads as 0
avrdude: safemode: efuse reads as 0
avrdude: NOTE: "flash" memory has been specified, an erase cycle will be performed         To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "I2c-debug.hex"
avrdude: input file I2c-debug.hex auto detected as Intel Hex
avrdude: writing flash (8684 bytes):
Writing | ################################################## | 100% 1.20s
avrdude: 8684 bytes of flash written
avrdude: verifying flash memory against I2c-debug.hex:
avrdude: load data flash data from input file I2c-debug.hex:
avrdude: input file I2c-debug.hex auto detected as Intel Hex
avrdude: input file I2c-debug.hex contains 8684 bytes
avrdude: reading on-chip flash data:
Reading | ################################################## | 100% 0.95s
avrdude: verifying ...
avrdude: 8684 bytes of flash verified
avrdude: safemode: lfuse reads as 0
avrdude: safemode: hfuse reads as 0
avrdude: safemode: efuse reads as 0
avrdude: safemode: Fuses OK (E:00, H:00, L:00)
avrdude done.  Thank you.
rsutherland@pi3:~/Samba/RPUno/i2c-debug $ picocom -b 38400 /dev/ttyAMA0
picocom v1.7
port is        : /dev/ttyAMA0
flowcontrol    : none
baudrate is    : 38400
parity is      : none
databits are   : 8
escape is      : C-a
local echo is  : no
noinit is      : no
noreset is     : no
nolock is      : no
send_cmd is    : sz -vv
receive_cmd is : rz -vv
imap is        : omap is        : emap is        : crcrlf,delbs,
Terminal ready
/0/id?
{"id":{"name":"I2Cdebug^1","desc":"RPUno Board /w atmega328p and LT3652","avr-gcc":"4.8"}}
/1/id?
{"id":{"name":"PwrMgt","desc":"RPUno Board /w atmega328p and LT3652","avr-gcc":"4.9"}}
Thanks for using picocom
rsutherland@pi3:~/Samba/RPUno/i2c-debug $ 

So this seems to have worked. The Pi cross compiler for AVR is older than the one on Ubuntu 16.04.