Created an account to write about a workaround to re-enable RGB lights on the ROG Ally, and there are a few extra steps needed but afterwards RGB works fine and you can cycle through the presets with HHD.
For me to rebase to this older build of Bazzite-Ally, I installed Fedora Kinoite 40 to a spare m.2 drive and then rebased that to the required version.
rpm-ostree rebase ostree-unverified-registry:ghcr.io/ublue-os/bazzite-ally:39-20240406
Basically went with option 1 listed in the Bazzite Installation Issues and Troubleshooting guide.
Once finished my Ally booted up, the RGB lights went to solid red and I swapped to my stock 512GB m.2 with a Windows installation, success all RGB features worked. Swapped the m.2 one final time with my actual daily driver of up to date Bazzite-Deck.
Thanks for the findings! I am unable to help test at this moment, but if anyone with an ASUS ROG Ally (any model) and wants to help out, then please get in contact with us here, on our Discord, or the open issue on Github for this. We would like to have this fixed this week since this issue lingers even when installing other operating systems on the hardware.