The board is designed to be partially populated.  The USB module has power and data LEDs, so the pwr LED is sort-of "underneath" that, if you're not using USB.  The 3.3V regulator could be omitted, with the 3.3v pad connected to the USB module (if you only need as much current as the ch340e can provide (which I assume is even less than the 50mA you can get from an FTDI.)

Thinking of moving or removing Aref; it's on the wrong side of the board (physically and electrically), I don't think anyone ever uses it, and the 4809 has more Aref options internally.

Added pads for most of the "unused" signals.  Not very big pads, but better than trying to attach wires directly to the lqfp, if  you really need one extra signal...

Those SMPS modules are tiny.   Theoretically, the board top layer is left blank underneath them, so that if desired one could replace them with "cheaper" linear regulation circuits.  But there isn't enough room for a full-sized TO220 footprint.  Also, the pins on the modules I have do not seem to be on any particular grid :-(

Added extra bypass caps on the bottom side of the board.  There is plenty of room, so...