I was in a similar position a couple of months back and had similar worries. I also didn't (and still don't) have the physical BSS certificate. It turns out that you don't need to send this with your license application, you just need the BSS cert number and the examiner PIN number. I rang CRT licensing and they were able to give me both of these numbers off their database after I gave them the name and registration number of my boat.
When I set off to bring her to my home mooring, I hadn't recieved the license paperwork (I'd only sent the forms off a couple of days before), so I kept a photocopy of all the paperwork sent in with me, just in case I got challenged for it.
As it happens, it took me a week to get to my mooring and I had expired licences in the windows the whole way. I encountered a fair few CRT staff along the way and none of them mentioned my expired licenses. Thats far from a guarantee that it's safe to just set off without a license, but I felt confident that my photocopies of the paperwork and a friendly smile would see me through as I'd sent the paperwork and cheque already.
Hope that helps a little
Cheers,
Andy