I'll take these point by point:
1) Dudley vs. Towns. This is a function of Towns not being in the league for all three years. I gave him (and other guys without 3 years of data) a zero for missing years. Just looking at this year, Towns is far ahead of Dudley.
2) Nogueira vs. Beal. This is a per possession ranking, not a measure of overall value. I don't see an issue with having them about on par per possession - Beal just plays a lot more minutes, so he has a lot more value. Nogueira has been pretty good while on the court as a high-energy defender however. Beal gets a bit screwed here by using a 3-year average, since he gets dragged down by the last two years.
3) DeRozan. The whole point here is that I don't think DeRozan is especially good, and that the Raptors have consistently been better when he's off the court. I think DeRozan's ranking as an average player is about right.
4) Whiteside. I don't see a big issue with Whiteside's ranking either. There's more to defense than spectacular blocks. He's a problem on offense meanwhile too, as he never passes, provides little spacing, and is a poor free throw shooter. He's a fun fantasy player, but his real life impact is much more questionable.
5) Batum. How good do you think Batum is exactly? A 0.8 RPM means he's about the quality of an average player on a 45-48 win team. That seems...fine?
6) Dedmon vs. Kyrie. This is sort of the Nogueira vs. Beal situation again. It's a per possession rating, not a value/MVP type ranking. Also, I know a lot of people ignore point guard defense, but I don't think that's correct. Kyrie is a bad defender, and has been his while career. If you don't think defense matters, your mileage may vary.
7) Jae Crowder vs. Paul George. Jae Crowder is a better player than Paul George. George isn't the same guy you remember who took LeBron to the wire in the conference finals.
8) Amir Johnson. Amir the anti-DeRozan. Teams are consistently better with him on the court, over a long career, across many different teams, teammates, roles, and team qualities. He's a very underrated player, although again, in low minutes. Giannis has a Beal issue in that the 3-year average is dragging down his breakout season. Blake's problems are well-documented meanwhile.
The overall theme here I see is that RPM puts more value on defense than you seem to, that these rankings are per possession, rather than overall value, and that it doesn't credit breakouts from young players enough (Towns, Beal, Giannis). I'm sympathetic to the last point - this was a quick and dirty average I threw together. The rest seems fine to me to be honest.
Insofar as we're evaluating DeRozan here, he's obviously more valuable than 132nd, since he plays a lot of minutes, but I don't see an issue with the per possession ranking really. He's a bad defender, and not as efficient as other high-usage poor defensive guys like Thomas.