Many/most of the C.Fn settings also apply to the C# custom settings...
Make that 'All of the C.Fn settings...'
Anything and everything saved to the C# custom settings is independent of what is set in any of the other modes -- as it should be.
All of them? So...that would include C.Fn III-8 on your 5DII, AF Microadjustment, right? Meaning, if you get a new lens, you need to go in and update that C.Fn for all your C# settings? Except....you don't, and that's certainly, 'as it should be,' in my opinion. I could go digging in the manual (IIRC there's a list of settings stored with C# modes), and possibly find others. But...AFMA is definitely not stored independently with regular and each C# mode, and that was the basis of my statement, "Many/most of the C.Fn settings..."