Roger the Rabbit I'm just not sure why they need to hold any back.
If they've sold seat 123 Row Z for Plymouth and someone wants a season ticket in that area and 124 Z is available then they buy that.
They could even sell them a season ticket for 123 Z but bar the season ticket for the Plymouth game and issue a paper ticket for a different seat.
I think there was a situation when they did the half-season tickets a couple of years back, where although you'd have thought they'd be sensible and not sell them for seats that hold been sold for the next couple of games....well, this is our famed ticket office here.
There's also the potential problem of one person buying 123 Z for Plymouth, and one person buying 124 Z for Palace, meaning neither can be sold as a season ticket (at least not without having to issue extra tickets etc). Reserve 123 Z as a season ticket seat and both those individual sales are made for 124 Z instead.
The idea about reserving a couple of thousand tickets is really just to prevent cock-ups. You shouldn't need to do it, but it ends the problem of seats potentially being sold twice by blocking them from general sale.