Haven't seen this yet so I'll go ahead and post it:
The builder doesn't seem to check for uniqueness between pilots and upgrade cards. If you try to add 2 of the same limited pilot, it removes the second one and pops up a message saying you can't do that. But you can add a unique pilot and also equip the crew of the same name to the same or different ship. For instance, I found it by accident when I was looking for a crew member to put on the Sabine in the attack shuttle. Sabine crew showed up as an option, and let me equip her when I tried. Same was true for putting Kanan crew on kanan pilot in the ghost. And a list with Darth Vader flying the TIE Advanced was able to equip the Darth vader crew on whisper.
Edited by VanderLegion