WOW! Thank you for the deep analysis, and for playing along with the thought experiment.
My thinking wasn't to find such a perfect solution like a full-on filesystem, but rather wondering whether the LittleFM idea could be extended to get some really rough utility out of the carts? Which is to say, what if you didn't worry about wasting most of the sector (#4)? So for example, a 2MB flash cart using the LittleFM method (in my limited understanding) would still leave space for 8 persisted songs (128kb sector * 8 in the unused 1MB following the LSDJ ROM) instead of 1. And what if we ignore carts that would make this difficult or impossible, like those without batteries(#2)? The carts that I'm playing with right now (2mb flash @3V, 32kb sram, readily flashable using Bennvenn's Joey) also have batteries and work just peachy with LSDJ, buuuut, are limited to the one song in work memory - precisely why I started wondering if the LittleFM method could be used.
But even if theoretically one could find the proper method to access the flash, (#1) through prior experience, reverse engineering, trace analysis + datasheets, or leveraging existing flasher code... it does sound like #3 is insurmountable. The Chinese carts I've been playing with are, as you say, either 3V or 1.8V. Hmm. I assume the carts that aren't battery-backed and have patched roms that write to the flash IC must do so through some programmer that can operate under, step down the 5V VCC?
I'm glad to hear it's crossed your mind as well, and thanks for writing back! Just kicking around the idea and trying to learn more about the hardware along the way. 
