Does being an athletic freak make you a better running back? Cuz the best of the best, to me, were freaks in one way.. vision.

It tends to help. The most important traits of a running back, IMO, are vision, agility, and elusiveness. The best RBs tend to possess at least 2 out of 3 of these. For instance, Lynch had mediocre agility scores, but he forces a lot of missed tackles and breaks a lot of tackles.
Michael is more freakish.
That is an opinion, not a fact.

No, no it is not an opinion. It is indeed a fact so long as Bob was referring to athleticism.
Judging a persons athleticism is an opinion, are you kidding me?
Nobody is saying the Combine is the ONLY way to measure freakish athleticism, but you seem to be trying too hard to dismiss it. It isn't ridiculous as you seem to be implying to have a level playing field as an equalizer in such a standardized set of tests and drills. Regardless of level of competition, team scheme, etc., they are put through the same paces, by position (including position specific field drills).
Let's back up for a second, this has been an unnecessary digression. Michael indisputably TESTED BETTER AT THE COMBINE (that is a fact, not an opinion), while it may not reveal every dimension of athleticism, it's the only standardized test we have. It can be useful in the case of players LIKE Keith Jackson (the GB TE, not the rumblin', stumblin', fum-BLE, Whoa, Nellie! one), who didn't get to catch many passes in the Arkansas scheme, or a player like Sammy Watkins, that ran a lot of bubble screens.
If you mean by freakish athleticism having a broad spectrum of physical abilities and talents that aren't captured in the net of the Combine, you need to offer something more than the too cool for school dismissals, that is like responding to someone stating 2 + 2 = 4 by saying, that's just your opinion. OK, well what is it than? Well I'm not sure, but that's just your opinion.
Maybe Tre Mason's athleticism manifests itself in other ways, who knows (he could be a tiddlywinks prodigy, which reveals information about manual dexterity, or a phenomenal badminton player, which could have implications for reactions and reflexes)?
It's common to call a player that blows up the combine at their respective position (or period*), a FREAKISH ATHLETE, its basically a convention within the sub-set of language found in the scouting community. If you have unconventional, unorthodox definitions of what a freakish athlete is and attempt to sow fuzzy boundary confusion on that basis, you are really just speaking to your highly personal, quirky, idiosyncratic (which rap rhymes with iconoclastic) definition.
There could be a situation where two people are in a concert hall, and one person points at the instrument with all the black and white keys and says that is a piano, and the other says, that is just your opinion, that instrument is a woo woo (nod to Bernie Worrell). The actual referent of the word piano is a psychotic, telepathic, albino penguin that is a Liberace Museum docent. If a lot more people understand the name of the musical instrument to be piano because it is CONVENTION that it is so, than piano refers to the musical instrument and not a psychotic, telepathic, albino penguin that is a Liberace Museum docent, despite any protests to the contrary from the person calling it a woo woo.
It might be more constructive to illustrate this with specific examples. I'll list some players that I think fall into the category of freakish athletes (though admittedly I have no idea if they are good at tiddlywinks or badminton). Feel free to comment, but rather than more too cool for school dismissals, bring some examples to the table yourself. A quick litmus test, though, do you think rookie defenders Clowney and Donald are freakish athletes. How about Calvin Johnson?
2014 Draft
DE - Clowney (similar 40 time to DeAnthony Smith, despite being about 90 lbs. heavier)
DT - Donald (broke the Combine record for a DT with a 4.68 40, also had 35 BP reps)
LB - Shazier (42" VJ, pro day 4.36 at 235+ lbs.)
Deone Buchanon was the biggest and fastest safety among the top prospects at his position (also unusual combo of blow up hitter with 15 career INTs), but I wouldn't put him in the same class. Justin Gilbert is also an extremely impressive athlete, but I don't think as rare as the above three.
RB - Jerick McKinnon (this year's Michael, clearly the freakiest freak at his position in 2014)
LT - Greg Robinson (some would say Lewan, but he is 20 lbs. lighter, Robinson's speed and agility were more impressive for his size)
WR - Donte Moncrief (6'2", 220 lbs., 4.34 40, 39.5" VJ and 11'0" broad jump, BUT, he may have hinky hands, which goes to show freakish athleticism in and of itself doesn't necessarily guarantee success on the gridiron)
Among active players, RG3 is pretty freaky (possibly could have been an Olympic caliber hurdler), Julio Jones, Vernon Davis, Julius Peppers (sixth man on a North Carolina team that made the NCAA tournament), Patrick Peterson (sub-4.4 CB speed in a 220 lb., borderline WLB-sized frame).
You asked, how could people like Michael better than Mason, which should tell you right there you may not think like other people. You were given a few suggestions, didn't address the oversight about Lynch being older than Stacy, and shot down the fact, not opinion, that Michael tested better than Mason at the Combine. Maybe these are related to some deeper, underlying, root misunderstanding. Obviously, if you are underestimating how rare of an athlete Michael is, that could be contributing to the disconnect in Michael's value between you and others. Just because you don't think Michael is a freakish athlete, you don't have to be so insular within your own welded shut beliefs that you are incapable of conceiving of the possibility that others might think that. Or, keep doing what you are doing, and continue to be vexed by the "inexplicable" thoughts and actions of others that aren't like you.
* Pittsburgh's Aaron Donald Was Your Combine MVP
by Chase Stuart
http://www.footballperspective.com/pittsburghs-aaron-donald-was-your-combine-mvp/
Bruce Feldman's 2013 Freak List (College)
http://www.cbssports.com/collegefootball/story/22278381/freaks-list-the-20-craziest-athletes-in-college-football