IPT, YES, I would have a high top if we were going to be primarily in Alaska. All of the major advantages we see in a penthouse would not be quite as necessary for us up there. We have traveled extensively throughout Alaska and the limited road system does not usually pose a problem with a high vs low profile roof nor is extreme heat a problem. I do agree with another member that posted concerns about snow and ice on top of the penthouse in the winter months as that could be a real issue for you.
All of that being said, it is only my wife and myself so we really only need one bed (vs 2 with the penthouse for the kiddos). The convenience of not lifting the top (and potential problems that go with a penthouse) along with the additional storage and cubbies that you can have with the high top would be a no brainer for our situation if we lived up there full time still.
You should go by
https://www.alaskacampervanconversions.com (as TomH pointed out) and talk to Charlie the owner. He usually has several vans in mid conversion to look at plus he can give you some ideas. He's a former boat builder and has produced some great work on Sprinters for friends of mine in Anchorage. He's not cheap by any means but all of his work is custom and built out of aluminum.
Zappo- I really appreciate the input regarding the dual generators along with the AC but we are hoping to not have to lug all of that stuff around with us if possible. 2 generators, gas cans, plus the AC unit itself all takes up lots of precious space on a 144" (not to mention the additional expense). We're also concerned about set up and generator noise. We will already have lots of "stuff" for longer trips including bikes. My wife & I are not KOA or any other type of formal campground people if we can avoid it at all costs. We enjoy being completely off the grid whenever we are traveling in my Jeep or Tacoma and have been known to travel great distances to make this happen. I am going to try and avoid the AC option if we can.