I think it depends on which person deals with your ATPL application at the CAA. I have just got my ATPL and a mate of mine got his a few weeks before me.
My mate had to produce a letter from his company to verify that his P1/S hours were genuine.
I on the other had was not asked for a letter from my company to verify my P1/S experience. Both of us did not have our hours stamped or countersigned. We both had very similar hours and both had more than enough P1 hours from instructing so both cases were very similar.
I was at the CAA getting a type ratng issued when I handed my ATPL application in and knowing of what happened to my mate, I asked the chap twice if all the paperwork was there (App form, Logbook, MCC Cert). He said that no other documents were required and he looked through my logbook before he took it and saw that my hours were not countersigned.
So in theory you might not need your hours countersigned but it did not make any difference for me!