So I tested it and the latest commit opens up in Ysmenu (Sakura gets whitescreen as usual), however it says bios not found. The checksum is correct, so it's the right bios, and it's on the root of the card in the GBA folder. X:/GBA/bios.bin.
The previous version that has working Mazes of Fate doesn't work, that one always shows whitescreen on Sakura, and whitescreen with text in Ysmenu and Wood (something like "RTFI on DLDI ver. 2.45 ab ab ab ab - the ab is in Greek). This happens even when I have the bios.bin on the root of the card (both in the GBA folder and the root)., since that older commit has a bug where you need to have it on the root of the card.
I do have a _gba folder on the root as well, and when I deleted it it appeared again when I restarted the DS. I'm not sure if it's created by Sakura or GBArunner2, since the date is always 1/1/2018 (I think it appeared after starting up GBArunner2, so it should've been created by GBArunner2).