When the truss nut is placed at the body end of the neck, the neck usually must be removed in order to adjust it (like some Fenders). You can make an access hole there, moving the pickup back some (as you mentioned). That can be hidden by a pickguard, or even a removeable section of the fretboard extension (among other ways). It shouldn't be a problem if you want to recess the rod a bit for more room. Just figure out where the peghead end of the rod will end up. Most of the effect of the rod is toward the peghead end anyway.
BTW, you might consider some of the other versions of the Hot Rod. Specifically, that is the reason for the "spoke nut" Hot Rod, so that it can be adjusted radially with a smaller access hole at the body end. Another idea is to access the rod nut through the neck pickup rout ... of course you have to pull out the pickup to do it ... which isn't much easier than removing the neck. Of course, you could also move the nut to the peghead end .... it's up to you.
If you use the 1/8" allen nut, you will have to have a big enough access hole to get the allen wrench into the nut (both in depth and length), and wide enough to allow more than 60 degrees of rotation of the allen wrench (you have to be able to turn it far enough to remove the wrench, rotate it one flat, and reinsert it for another bite). You will have to work out what that is in your case ... but it will be a fairly large amount. You may want to think about that part some more before you jump into building it.