Hi
Windows and Gnu&Linux can share the same config folder but you might need 2 versions of the extensions you use. You can keep both versions in the same folder as each other.
It is better to set-up the Windows side first and then get the Gnu&Linux side to look at the Windows config folder as the Windows side might have extra settings that are not needed in Gnu&Linux. Also Windows is blind to Gnu&Linux file-systems whereas Gnu&Linux can easily read/write Ntfs and Fat32, Fat16 and the rest.
I don't think it makes any difference after install but with Gnu&Linux there are at least 2 different installers; Rpm & Deb. It's the same source-code. Like the difference between taking your shopping home by car or bike it's all the same once it's on your shelves. I'm not 100% certain about this tho.
One note about splitting usb-sticks into 2 partitions. The Windows one (Ntfs or whatever) needs to be 1st on the stick and needs to be created 1st. If Windows can't find one of it's own partitions at the front of the drive then it assumes the drive is unformatted or corrupted. On normal ide/sata drives and internal SSDs it seems to be ok.
Anyway i think this thread was mostly about the various Windows platforms.
Regards from
Tom