A friend of mine who was on a long hiatus from the game once told me about how his FC would take turns logging in so they wouldn't lose their FC house even though none of them played anymore. In such a case, an FC owning the house means there'll be more people to help keep the land from being lost without actually using it opposed to a single player who might've used the heck out of that plot.
Then there's the fact that personal houses can be shared, making them comparable to certain small FCs with the exception of the FC workshop.

It's a complicated mess and you're going to find as many examples why FCs shouldn't get priority as you would reasons why they supposedly should.