While I can't say for certain, I would think so since it's like making two separate reservations. I would be very surprised if there was some sort of exception handling in jetBlue's system to not earn points on the second reservation, so you should earn points as if you had booked two separate trips.

For those of you confused, you can see jetBlue's instructions for purchasing an extra seat here.

It is actually interesting to me because I am getting close to the end of my Mosaic Challenge period and I am a bit short. I was thinking about tacking on an extra roundtrip with an immediate turn (say JFK-BOS-JFK) when I return to JFK from PHX in a few weeks, but now I'm thinking I should just look to see whether I can purchase an extra seat on my PHX-JFK segment if that will put me over the top. It has the added advantage of not wasting a few hours flying to BOS and back.

Curious to hear other's thoughts on this.