Mike,
You know, in the beginning, I liked the numbers of the Yamaha units, but the size, weight and shape did not fit into any scenairos I could build myself.
Portable A/C units are specially designed to have low amperage draw starting compressors. This reduces the size of the genset you need.
I am now using an 11,000 BtU A/C unit that will start with a Honda i2000 generator running in Economy mode. That is around a 9 amp starting draw.
I don't think you'll find many rooftop units operating at that low a starting draw. yes, they do make special rooftop units like that, but they are heavier, need special mods to your boat, special wiring, etc.
As far as getting on and off the boat from the transom, I have had no problem with that be it while camping on the hard in transit or anchored in the water. The genset box is not as high as the transom and you have to get your legs over the transom, so there is no greater effort involved than if there were no genset box. In fact, it is easier in rough seas since you just sit down on the genset box and rotate your feet over into the cockpit with no need for delicate balancing.
I like the genset so I can run cooking appliances, TVs, charge computers, etc., not just for A/C. It relieves me of having a huge Inverter setup with heavy extra batteries to maintain, yet I always have backup power. The Honda i2000 has a built in charger system with an outlet and battery charger cord set.
In any case, the genset box only needs 4 bolts to remove or install - no holes, no fiberglassing, no external wiring. You just plug your 30 amp shore cord into the genset socket. The generator simply sits in the box with no screws/bolts, so all you have to do is lift it in or out of the box. The box has a lock so theft of the generator is minimal risk and you can put other gear in there if the generator is not in there.
The Honda i2000 sucks cold air in the front and blows hot air out the back along with the exhaust, so putting that hot air exhaust out the big flap is safe and leaves a cool, well vented casing for the generator. I am at 3 years of use now and have had no untoward experiences with this setup.
The A/C unit I use now is not the one pictured in Tom a Hawk's album, but it is held in place with ONE rubber shock cord, can easily be moved on it's built in wheels, and can be moved and mounted in 3 or 4 different places inside the TomCat cabin.
So you have more options with fewer needed modifications and NO irreversible changes in your boat.
John