485, 765(EAD), 131(AP) of the same person can be in one envelope. In fact, it's assembled in a single package with a single cover letter in my case, with no duplicate documents for 765(EAD) and 131(AP).
Three separate case numbers for 485, 765(EAD), 131(AP). For future renewal, each time it will has a new case number. (Your alien number on the form should stay the same though.)
For my case, my spouse's application was in a separate envelope.
(Our cases were approved)