I think that's a reasonable if somewhat misguided policy, I've worked in coffeeshops and I make sure I buy something every half hour or so (not good for the waistline) since I'm occupying space they are paying for.

I actually wish they'd work out what a fair market rate is for someone occupying that desk, throw in unlimited coffee and just charge me by the hour.

If it gets really busy I clear out since they can make more turning over tables than with me sat there, I've noticed by doing that and not pretending to own the table I'm sat at the coffee shop owners are friendlier.

If there are empty tables, it's fine to sit as long as you like. If there aren't empty tables, it's common courtesy to eat and go.

Seems straightforward to me.

This is true, consider that having patrons sitting in your shop attracts others often enough that they will appreciate you being there if its empty. If it gets full though, buying stuff and leaving when you are finished is good form.