Thanks to Tanooki now on the Digital Press forums, he brought us an early build of the new Retron 5 firmware to try from Hyperkin. This is firmware version 1.41, but it covers the features I listed yesterday, and it also now adds the ability to
save GBA games with EEPROM memory back to the cartridge. I downloaded it and tried it with Ultimate Brain Games and a decent save progress file I had on Super Ghouls & Ghosts (both EEPROM games), and both games wrote the new progress I made on each game back to the cartridge successfully, having tested them on my GBA SP after saving. I had no idea about half the games in the GBA library used EEPROM save memory, but it's used primarily for smaller saves and high score saving.
You can download it
here, but keep in mind this is not an official version of the firmware. It's a test/development build, and not all the fixes may be working.
They are also working on a way to reduce the startup times to about half a second after pressing the power button, compared to the 4-5 seconds we have to wait right now. I wish them luck on that, so far it seems to be a success!