Are you running aero brake levers? You could start by running non-aero old school brake levers, where the cable housing doesn't go under the bar tape. Then you'd just have the bar end shifters, and you only route those part way under the wrap, right? As in, they emerge from the wrap when the flat of the bar starts to curve up, right?

A lot of modern handlebar wraps don't adhere to the bars in the same painful way that they used to -- look for any wrap that has kind of a gel adhesive bonded to the backside, instead of a white wrapper strip to pull off. That'll make swapping wrap easier.

I'd say by the time your cables and housing wear out, your wrap is probably due or overdue.

ALL THAT PRACTICAL STUFF ASIDE, I admire the crazy spirit to try to innovate, put yourself in danger and maybe destroy parts of your bike. So here's what I'd do: if you don't want to run non-aero levers, you're right that internal routing through the handlebar is going to be a bit tricky. You'll have to drill four holes for the brakes. One on each side close to the base of the lever and one one each side as far from the stem as possible while staying out from under the tape. If you have a Madone 9 laying around, take a look at those handlebars. The cables -- both shift and brake -- emerge from a hole on the inner bend near the base of the hood. There's a second set of holes on the outside of the bend near the hood to help you fish cables. So maybe consider drilling six holes. You've got the drill out already -- why not use it?

It will be, as you laid out, a multi-step process when you change housing, because yes, you will need the old cable to guide the new housing as you push it unseen back into the brake lever base. Then you can switch cables, but pray it doesn't accidentally push the housing out of position. That will be a hassle.

For the brake holes near the stem, I'd put them on the bottom side of the handlebar, because it will experience more compression force, and be less likely to crack -- or so I imagine! Who knows! But it will make the cable routing a little neater, since those cables are headed down anyway.

The shift cables, that's just a simple hole at drop right where it starts to curve up. You don't use the drops anyway, do you? No danger there. Drill away. A lot of those touring bars are so thick and burly, you could woodpecker those things and they'd probably be fine. Frames get drilled all the time -- for routing, bottle bosses, you name it. I bet anything Rivendell or Nitto make could take a lot of shots through the hull before heading underwater. But that's just my ignorance making a guess.

Good luck with your project!

If it takes five years or so, that's cool, but come back and post some pics, an obit, or whatever you end up with.