There isn't actually a rule about this - it's just another of our 'traditions' that members of the same party sit together. I suspect what will happen is Labour will fill up the whole 'Government' side - then start down the other side from the end furthest away from the speaker. Then the Tories (or Lib Dems!) will be opposite the Labour Ministers by the speaker - with the Lib Dems (or the Tories!) in the middle of the opposition side.If that actually happens where do they sit in the commons. Do they all squeeze onto the govt benches? They'd be squashed in like sardines, looking at half empty benches the other side.
Minor issue I know but these admin type things bother me
Then again, only about 2/3 of the MPs can actually fit in and sit down at any one time anyway.