As covered by the previous replies to your leading post in this thread . . . there are little differences aside from the added comfort and protection provided by the pilothouse. I am not too familiar with ALL the pilothouse choices out there, only with the one my wife and I recently bought . . . a Nauticat 33 motorsailor. We absolutely love the boat''s build quality, interior liveability and outstanding teak joinery. The standing and running rigging is also of a high quality. The interior space actually seems bigger than most 40 footers I''ve been on.
Irregardless of what some sailors think about the appearance of a pilothouse, I really do like the traditional lines of Nauticats (did someone actually say pilothouses were "ugly" in a prior reply?). There is a lot to be said about not having to deal with dodger canvas and issen glass.
With a 90 hp diesel, I can motor upwind, in no wind, or against currents at 8-9 knots. However, it is still a sailboat, although comparatively not the fastest ketch, she sails pretty darn well for her size.
If you are interested in pilothouses and in terms of basic differences between boats with cockpits . . . it is important, in my mind, to have an aft station for nice weather sailing or motoring. When things get snotty, go inside. Sliding teak pilothouse doors on both starboard & port sides make deck access easy. A large sliding moonroof makes checking sail trim convenient. The aft deck helm is also the preferred station when sailing in tight quarters. Therefore, we have versatility with both a cockpit and a pilothouse.
My wife is a total sailing novice, but with autopilot (we have a handheld remote), I can singlehand the boat even when tacking, or trimming the sails. Eventually, my first mate will be more confident to take the wheel, usually the arrangement most couples in our situation lead to.
The bottom line is what feels right to you and the type of sailng you prefer and expect from your vessel. Motorsailors & pilothouse sailboats are not designed to be fast race boats, but are extremely comfortable and versatile cruisers. JMO