There's basically zero possibility that water could make it from outside the car through that hole in the firewall that you use for JB4, meth controller, reflex or anything else. I have the Verus hood louver installed with a hole cut in my hood, and there's no way water could get back there.
Drilling the hole in the back, you mean? That's what I did for the meth controller. It's not a big deal.
That said, you can route the wiring in from the gromet under the cowl. Remove the glovebox to run your wiring/install the gauge, then reinstall when you're done. Pretty easy job, honestly.
We care that you're enjoying the new ride! These things are monsters, even in factory form. A lot of folks seem to forget that quickly and go mod crazy right out of the gate. The back end tends to get squirrely with VSC off, so be careful until you get a little more familiar with the torque...
Live without flex like we did for the last 20 years? This is a giant fucking nothing-burger as far as I can tell. We've been running different maps that adjust timing, boost pressure, whatever.
Motec/Haltech whatever is always an option too. I really don't get what all the fuss is about.