Milo,
The aircraft with a hatch with 20 plus different lengths of screws is - Typhoon. That aircraft had an equally massive (but unreported) weight problem during development. Actually, most combat aircraft have a weight problem at some time. STOVL brings it into sharper focus as the weight vs. thrust equation is fairly black and white.
I can tell you that every panel on JSF was carefully looked at to get weight out, and the teams doing this had a lot of input from highly skilled and experienced maintainers.
The best solution from a maintenance aspect would be one size of fastener over the whole aircraft. Not practicable, so the next best choice is one size in one panel. If you can't bear that weight, things are more complicated and you end up trading fastener size and length - neither the best choice.
On one JSF panel I remember we ended up going for two different fastener sizes, far enough apart to make it harder to use the wrong tool. JSF has lots of panels (good for access) so lots of fastener issues to address.
As far as the multiplicity of nozzles, hatches and covers go, well that's what you get when you ask an LO supersonic aircraft to have a minimum flying speed of zero. I have to admit to getting ever so slightly miffed when people get sarcastic over that truth.
I suppose what I'm trying to put over is that the JSF team have done their level best to cover all the angles and meet the specs. The most onerous specs were in the areas of logistics and maintenance and they have spent a shedload of time and money to get to the best answers they can. They have also used highly talented people. Have they got everything just hunky dory? No. Have they done damn well? Hell, yes.
Best Regards as ever
Engines