Both PFA aircraft (some of which are microlights just to confuse things) and BMAA microlights operate under the Permit to Fly system. In both cases the conditions of flight are more restrictive than for C of A machines as you've noticed.
The overflight restriction applies to 'congested areas'. This is a term which generates much debate, but I don't know of anybody who avoids tiny hamlets as a result of it. A good working definition is to avoid flying over any of the yellow bits on the CAA chart. That can be a slight nuisance, but it certainly doesn't stop one from travelling.
Trips to La Rochelle etc., are in practice hardly any more difficult to achieve in permit aircraft than in CofA ones. Unless they have full instrument ratings, pilots flying CofA aircraft, while they can fly over towns, still have to remain VFR at all times and so are still totally dependent on the weather. Avoiding built-up areas in the wide open spaces of France is not usually a problem.
There is no problem with microlights flying outside the UK, in fact more than one has circled the globe. France has given blanket permission for UK Permit aircraft to operate there. Some countries haven’t, which means getting permission in advance and sometimes paying a fee. That’s a nuisance too, but again it’s not too much of a hurdle.