I belive I finally figured out the problem! There was a problem in the code and the variables were not being saved properly, it worked if you just went forward straight, but if you loaded the game or used the history it would erase the proper state for those particular variables. Check this build out and see if it solves the problem for you!
Build
I'm not entirely sure I understand the problem. You need to play the scene for it to show, and the progress you make is saved separately so if you save before a scene with variants and load back to play all variants all of them are going to be unlocked, this is kept on a separate file and is independent of your current save. I would need to start a clean save to test all of the scenes you are saying are missing, but I did test with the Evelyn scene, which I hadn't unlocked, and some of the variants of others scenes, and they showed up properly on my gallery. Though Evelyn scene was indeed not showing on the CG gallery and I fixed that.
I'll eventually delete all my saves and do a clean full run to check the other scenes you pointed out, but that will have to wait for the next release as it will take quite a lot of time and I'm already behind on my schedule with all the bug fixing I have been doing these past days.