All the things about Ganon you mentioned are true, but I want to emphasize the fact that I think Bowser has every tool Ganon has, but with superior mobility to execute it (command grab, spaceable aerials, etc.) -- minus the gimping capabilities, but despite Bowser's linear recovery, it's deceptively difficult to intercept, because DAir is ordinarily too slow to snag him, and for UAir to be useful, you have to be under him, which requires positioning, such as being right on the ledge as to position yourself before he reaches the ledge. In theory, a linear recovery, a meal for Ganon boot makes. But it's circumstantial, like with DK's.
Fair, in my experience, is actually the easiest aerial to hit him with offstage, because if you space it right, it covers all options. If he doesn't use Fortress/double jump, he gets hit with the late hitbox, and if he does, he gets hit with the early hitbox, and it kills him at around 60% without rage if he's already offstage. It's that good.
The one important thing to note though, is that even if our aerials beat his out by a fractional margin, almost everything we do short of UAir is commital. Almost none of Bowser's spacing tools are commital or leave wide openings. We beat Bowser in the air when Bowser's willing to approach. But in high-percent neutral situations, Bowser has a lot more ways to safely kill us than we do him.
My experience differs considerably. His tilts are just as laggy as Ganon's, and pack slightly less range to boot. His aerial options more consistently auto-cancel, but seeing Bowser jump into the air is a very telegraphed action that also opens him up to the easy hitboxes of Ganon's fantastic up-air. Bowser might have speed, but he has a LOT of inertia once he's in the air, so once he's going in a direction, he's going in that direction, making reads very easy. Bowser's aerials are only non-committal if you assume Ganon has no option other than "press shield". Ganon can very easily challenge Bowser's aerials with his own and not even end up trading.
Two things I just found out with a bit of testing: 1. jab 1 to fortress is a true combo that deals 13% It works at every percent too.
I can't replicate this at all. Jab1 knocks Ganon far enough away that it doesn't work past 0% for me, and it only works then if you're within Ganon's grab range. Might be because I only have 3DS, but either way, as you said, it's irrelevant and probably even a bad idea, since fortress has awful endlag, while Jab2 does not and has similar power.
2. FAir beats out our up-b. Keep in mind, it reaches all the way below Bowser. That means Bowser kills us off-stage almost as much as we kill him.
I was able to replicate this, but only if timed exactly right, and only if Ganon starts the up-B near Bowser's front, which is within range of Ganon's fair. It's very difficult to time. In actual games, I've been able to challenge Bowser's edgeguard with Ganon's fair while recovering in the past and ended up with the kill, still able to make it safely back to the stage. As long as you aren't desperate for the up-b, Bowser is taking an exceedingly unnecessary risk if he decides to edgeguard Ganon. Bowser's back-air does outrange fair, but if you see Bowser setting up for it (jumping off with his back turned), he's vulnerable to up-B again. Bowser doesn't have mixups or options that cover everything in his edgeguard game like Ganon does. Bowser's down-air will spike himself if he's offstage, and his up-air is all but useless anywhere but directly below Ganon, where Ganon is deadliest.
But I'm not saying it's an outrageous disadvantage. 55:45 at max.
I still think you're giving him too much credit. If Bowser does have tools in this matchup after all, then it's probably an even 50:50. Give Ganon some credit where it's due. Bowser's good, but this is a matchup where we really get to cut loose for once. I'm sticking to my guns at 55:45 Ganon's favor.