You make a lot of really good points (and I'm not just saying that to be nice), but they're missing the bigger picture: the monopoly topic only matters if Apple did the rest of what the plaintiffs claim, which they clearly didn't.
To break it down further, here's the chain of arguments the plaintiff is stringing together:
1) Apple never added support for other app stores
2) As a result, the App Store had a monopoly on app stores
3) As a result, there was less competition between apps
4) As a result, app prices were inflated
5) As a result, customers paid higher prices
6) Ergo, Apple harmed customers by never adding support for other app stores
If any link in that chain fails, the case falls apart, and to me, #3 has the biggest problems. Namely, less competition between app stores doesn't necessarily equate to less competition between apps, which should be patently obvious, given that there was never anything stopping Developer A from competing with Developer B in the App Store. Anyone can develop a competing app at any time, without Apple having any say over pricing.
And I'd like to come back around to this question, since I think it's worth addressing...
Why, then, do you you believe that those completely disparate app markets should be seen as a single market? That just doesn't make any sense at all from a legal perspective, even though people keep claiming otherwise.
The reason I think differently is because I've seen the courts rule differently in similar cases. I'm not going to argue for it, but I will try to explain it.
Remember the Apple eBooks price-fixing case? Apple paired an agency pricing model (i.e. publishers get to set their own prices and Apple takes a cut) with a Most Favored Nation clause (i.e. publishers agree to give Apple their lowest prices). The courts ruled that pairing those together amounted to price-fixing, since any cut Apple set for itself would effectively be forced onto any competing retailers in the eBooks market, preventing them from competing with Apple on price.
In a far away bizarro world, a fictional version of you cries out, "But wait! iBooks have to be rewritten for Apple's platform, are locked to Apple's platform, are sold through Apple, and switching to alternatives would require purchasing additional hardware, so it makes no sense to treat them as part of the more general eBooks market. They're their own iBooks market." And yet, despite those points, the courts clearly thought Apple was competing in the eBooks market, hence why they had competition that they could illegally influence. Had they been in their own market, there would have been no competition.
If the courts thought Apple's iBooks were part of the larger eBooks market, I don't see why iOS apps wouldn't be treated as part of the more general app market, given that the situations are nearly identical from a business perspective. Again, I think you made good, compelling points, but I'm forced to admit that the reality of the situation appears to be different from what you've said.