Originally Posted by curio
Because it's cleaner that way.
It's the same book
If you have it formatted a different way for different devices, you'll want to tag it differently ("an original PDF and one post-processed for small-screen devices"). Tags are associated with the book record, not the formats within that record, so for that to work, you need separate book records for all of your "post-processed for small-screen devices" formatted books.
However, one thing I've learned is that everyone has a different way of doing things that seems "right" to them. Fortunately, Calibre can accommodate most of them.