Ideally you only rebase your own commit on your own feature branch, just before merging. Having a clean commit history before merging make the main branch/trunk more readable.

Also (and especially) it make it way easier to revert a single feature if all the relevant commits to that feature are already grouped.

For your issue about not knowing which branch the commits are from: that why I love merge commits and tree representation (I personally use 'tig', but git log also have a tree representation and GUI tools always have it too).