There's a limit to how 'custom' the factory can do. They can do simple changes - omissions are easiest - but even simple things like different binding materials have stumped them or been ignored. I've had P90 routs done on an ES-1 rather than the standard humbucker ones, but they've got the template for that, so it's doable.

As the PSH-1 appears to be of an all-hollow body construction with a solid centre block, I'm not sure where you'd get more body routing done (though I may be wrong). If so, it's not like a Tele thinline construction where a larger rout is an option. I do have a very similar shaped kit body with a mahogany body and the chambers in that are very large and not just a bit bigger than the f-hole area but run all the way forwards and backwards.

I agree that those big F-holes are fugly and ruin the looks of the body for me. As long as the factory that makes the PHS-1 also does the ES-1 styles (or similar,) then that smaller Gibson-style of F-hole should be doable, but PBG get their kits from several different factories, so there's no guarantee here.

Not at all sure about a different scale length. I'd imagine that all the set-neck guitars are 24.75" scale length, so it would be very custom. And as the kit is already drilled for just a T-O-M or wrap-over bridge I wouldn't guarantee that they'd move the post holes back a bit to compensate for the scale length change. If you don't tell the factory exactly what to do, every little change required, they won't think for you, so you'll get them in the same (now wrong) position.

A mahogany body could be a viable option as they should have mahogany blocks available for the solid body PRS shaped guitars

It's always best on custom orders to have an email conversation with Adam to see what he thinks the factory can do. But the factories do tend to say 'yes' to everything and then present you with a kit that can be missing several vital changes. If the factory get it wrong, then Adam is very good and will let you know and you don't have to accept it. But it's not like a Fender or Gibson custom shop, as everything is done on the main production line using routers and templates. They won't create a new jig or template just to do one guitar.