While browsing the website I ordered the flash chips from, I found they offer a line of SD NAND Flash chips other than the series I just ordered. These are interesting as they're higher capacity, cheaper, and the same for factor. 

Here's a 64GB for $14 USD: 64GB flash.

I Just paid $11 USD for an 8GB flash chip, so that's a little annoying. My fault for not doing enough research. I did order a part that is confirmed to work how I want, so it's ok. I'll order a few of these chips for testing later. The per part price is still quite high for these chips, but far more reasonable than an SD card with a socket. More reliable connection as well. 

They also offer a cheaper 1GB flash chip. This is around half the cost of the one I ordered, which is nice. I need to determine the trade offs between the two series of chips before I make any decisions. I'll solder headers to the prototype HAT and the SOIC breakout boards so I can swap chips easily and test everything out thorough. 

Having cheap 1GB chips has me considering adding one along side the larger chips. The smaller chip could load the program and be read only, while the larger one could store user data. That might make it easier to protect the program data from corruption and accidentally being erased. I'll wire up two cards on a board and play around with the software in the near future. One will have to be over the SDIO interface, the other in SPI mode. SPI is far slower than SDIO, but I've ready reports of getting 4MB per second on it. I plan on designing loading screens if I can implement them. Fun animations and even mini games may be an option. I don't think slow loading times will hurt the experience too badly. Especially if loading retro style games from a cartridge. We shall see.

I've been really disappointed in how slow progress on this project has been. Life has been crazy and money very tight. Having finally ordered the hardware is inspiring me to really push forward on this. I still don't have much time to dedicate to it, but progress is being made. Feeling a bit of imposter syndrome these days, being stuck researching and only talking about the project. Next week should change that when most of the hardware arrives and I go pick up my first Pi 400.