While Mewtwo's standard ledge options may be mediocre, his true ace in the hole here is all the things he can do out of a ledge drop, like airdodge, attack, confusion to beat shield etc. And that's mentioning he can often bypass the ledge game entirely easily against certain characters, especially with a charged shadow ball as backup.
Against Doc, while it's true Mewtwo has to respect his options, they're rather easily avoided by simply not being reckless and spacing correctly. A well-played Mewtwo won't feel all that different to fighting a swordie with Doc, as he struggles to even get the trades you mention. He may cause more damage with single hits, but that's likely all he's going to get, while Mario can easily get more with his mobility causing much more damage overall.
Doc can't really edgeguard with Tornado at all either, or even get to play the ledge game often since he's so slow Mewtwo can often bypass it with little worry of having his landing pressured. Conversely, of course, Mewtwo has relatively little trouble gimping Doc with how deep he can go.
All in all, Doc pretty much can only really exercise his power and close-quarters speed if Mewtwo makes a mistake, whereas Mario has the mobility to exercise it often, and with relatively little pause, also letting him land HIS kill moves with greater ease (which includes things like dair, bair, and even his inferior usmash). The only question I have is if dthrow->fair is a thing, because otherwise Doc hardly seems to get anything meaningful from a grab against Mewtwo (except bthrow kills), not even positional advantage. You said as much by mentioning Doc couldn't trap Mewtwo.
Just keep in mind 40-60 for me means a solid advantage, but the losing character still does have things the winner should be wary of, like Ganondorf's sheer power or Kirby's amazing CQC. For Doc it's his meaty moves preventing Mewtwo from ever being reckless.