I'm a little puzzled by your post... short version is of course COBRAS lets you do this - I've done it probably thousands of times and I know many customers who precreate users (without messages) using COBRAS and then the night of cut over do imports of messages using this technique.
The only reason you'd have to pick a specific user on the conflict resolution page is if the alias/extension did not match properly (i.e. you created/imported users from a different source or by hand ahead of time) and there was a conflict or the users could not be found by alias/extension. If you did the import with COBRAS and then imported again with the same database it should always line up perfectly.
are you SURE you are REQUIRED to select users? COBRAS will always show you users it will be overwriting in yellow just so you can review - this is ok - you can just hit next and move on, no need to touch each user. If they are in RED and marked as conflicted then you have to take action. The only three states it shows are:
1. create new (green)
2. overwrite existing user (yellow)
3. conflicted (red).
The only one you MUST take action on is red.
So please take a close look when you run through it and maybe post a screen shot - it may just be that you're assuing because it says overwrite and is yellow you have to then go do something - you really don't.
