Is there likely to be any problem in pointing different annexes to the same special remote (i.e. rsync/box.com/etc.) ?
As the objects are stored based on their SHA256 key the expectation is that the chance of collision is is small.
The only problem I can foresee is where the same content is stored in more than one annex and it is deleted in the remote in one annex, but not the other - there won't be any protection against that, but for non-overlapping content this risk should be negligible.
You're basically right. Additionally, if you use encryption, the keys used on the remote are themselves encrypted and so even the same content will result in different keys.
With this said, it's easy to use a subdirectory of a rsync or box.com remote, and I'd rather recommend doing that, rather than jumbling multiple repositories data into a single directory.