As others have covered, the neck pickup needs to have the 24 fret option applied, otherwise your 24th fret is going to overhang the pickup route and you won't be able to fit the pickup in.
As for the 720 mod, it does help high fret access in that in means the total depth from the very back of the pocket/heel to the very tip of the fretwire is slimmer. However, it's a difference of only about 2mm. If you couldn't reach around the heel before, the 720 mod won't make it any easier. It's really there for the aesthetics, not function. Speaking of which, though the total wood depth is smaller, your strings will usually end up having to sit higher since the bridge isn't lowered as well. It's roughly the same kind of distance difference as you get with a non-recessed Floyd, i.e. the neck has to be angled or you have to have higher action, pick your poison. I do like and often order the 720 mod for the clean look with fixed bridges which are easy to work with, but I wouldn't bother with any vibrato bridge; it's too much of a hassle to then get the heights of everything else all matched up.
All that said... other than the inlays, there's nothing on your list here which you wouldn't get from a standard Mayones, Ibanez, ESP, Schecter, Jackson, Charvel, Kramer, etc guitar for a lower price, even at the same MIA/MIJ quality. Seems a bit odd to me to bother with the cost and hassle of putting together a custom parts build for something which, fretboard inlays aside, is so standard. A black HH superstrat with a Floyd and a thin neck hardly suggests "had to go custom". Unless having the skull & bones is that critical to you, you should probably take a closer look at existing models out there, or go more custom with Warmoth to really justify the effort. I've put together a few friends' rather pedestrian orders and every time they've been happy with the resulting guitars but openly questioned why they bothered vs just buying a regular Fender or PRS or whatever. Of my own Warmoth (and/or other parts companies) builds, I also started off making the most run-of-the-mill guitars and all of those I ended up ditching, separating out and reselling the parts of; the ones I've kept have been the real custom jobs, bodies and necks which are completely different to what you can get off-the-shelf. Especially when someone is questioning their own build so much, it just makes me think a regular production guitar will likely be more worthwhile for you.