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#11
There was a time when I was dual booting Windows 98 and Windows 2000. Windows 98 was installed on partition 1 formatted as FAT32. Windows 2000 was on partition 2 formatted as NTFS. Windows 2000 saw itself on D and the Windows 98 partition as C. Windows 98, not recognizing NTFS, saw only itself. Installation of Windows 2000 was started from within Windows 98 and directing the installation to the other partition. I don't remember having any problems due to this configuration.
Well written software doesn't make assumptions about where things are installed.