Yes, of course, a new rubrail would present the same issues with holes. Doesn't mean it can't be done - just something to address.
The deck fits over the hull like a shoe box lid. That happens behind the rubrail. So the bottom edge of the rail will typically have an extra lip on it because of the "lid".
I haven't met a rubrail yet that I haven't been able to make look better. You may just need to be more aggressive (using a PROPER buffer). Once you get rid of the top layer of UV damaged PVC/Vinyl, the underlying material is still good. I've heard some have had some luck with acetone - but you need to move quickly since it basically melts the rubrail. I do not know how long that method lasts, though. But keep it protected with 303 and that should help.