The registry editor indeed works with Windows NT/2k/XP/2003 registry only. The reason is that BART is based on Windows XP, so it is capable of working with NT-based registry; it is the function of the operating system itself, so it's the same code you are using every day to access your registry; you can be sure that your registry will not get trashed anyhow.
The format of Windows 9x registry, however, is different. You can't attach Windows 9x registry in an NT-based system. The format of the registry files is not documented either, so it's quite hard to write a code to work with the registry files. Sure, you can do some reverse engineering and hope to find out enough information to describe the format properly... but it will be a big "hack", probably with a number of "unknown" fields.
Well, not that I wouldn't be thinking of it

, but it certainly may cause nasty problems...