As you say, interesting times ahead.
I would have thought that the teams of negotiators would have thought about such issues and party conferences and by-elections, but I cannot think how they will resolve such issues - possibly who has the biggest electoral vote in a particular constituency stands unopposed by the partner in government?
It may well be big, short term gain for the Lib-Dems, but it may prove their long term downfall too, losing their independent identity, and if anything reinforcing the traditional Labour vs Conservative loyalties amongst the electorate.
As you say, the chasm between the Conservatives and Lib-Dems over particularly PR and electoral reform, and also Europe, seem very very difficult to reconcile.