I got it to work! You need to create a directory in /atmosphere/titles/ called "010021C000B6A000"
then create a directory inside of that called RomFS, and inside of that directory put everything on the inside of your converted folder (except for anything that refers to workshop or metadata, that can stay back)
Then boot LayeredFS and you should be good to go if you start Isaac.
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@Sasori if LUA Mods could somehow be implemented, that would be amazing...