technically the 2K box would be joining the 5.5 site but that's neither here nor there...
2.4.6 will not be able to get at mailboxes homed on Exchange 2000 server at all (the MAPI login stuff is just different enough to cause problems). AD replication can only be one way (from Unity's 55 out to AD... not back) or you'll trash your data.
Short story - not really and it's not a good idea to try it.
I'd strongly reccomend getting up to 3.1 and going mixed mode if that's what you want to do - shoe-horning 2.x into this environement is just asking for trouble.
For the first issue where it told you the Windows version was too low, make sure you are logged on to the computer as a domain account, I believe I have seen a similiar error when attempting to install Exchange 5.5 on an NT box when I was mistakenly logged on to the local computer and not logged on as a domain account.
Are you getting this error “Installer User Interface Mode Not Supported. The installer cannot run in this UI mode. To specify the interface mode, use the -i command-line option, followed by the UI mode identifier. The value UI mode identifiers...
The below trick might come handy when you have to add a new node to a cluster but you don't have or is unsure of the security password for the publisher. This procedure has been around for ages.
1) Login into the CLI of the Publisher.