I doubt any of it was factory, when I say old I'm talking 30+, although some of them were factory undersealed. Never done it myself, well, a few times in areas but not an entire underside. Just applied by brush or spray/injection depending on job.
I don't think drilling a hole in a panel and injecting waxoyl, then putting a small body-coloured plug in would be noticed, or invalidate a warranty.
Why not ask your dealer? I'd be very suprised if you have any issues though, unless the thing's built from tinfoil. Our Cherokee was new 7 years ago and the underside's still really clean, even though it's barely ever washed - and it gets used a lot in winter.
The new stuff they use on the roads is pretty aggressive though.