I've seen some discussions on those points - I was of the understanding (please correct me as necessary) the third-party replacement was dependent on grabbing vehicle-specific certs off the existing MCU hardware (which was not guaranteed to be available) and only possible if the MCU board was physically on the third-parties bench (which may be a non-starter for some owners).
As far as number replaced, I have not seen any stats to claim a majority of warranty vs new vs refurbs.
I haven't seen any hard data either (doubtful Tesla will release that unless the class action lawsuit goes to discovery) but through reading posts here it seems that most are covered under warranty and I'm sure many don't even bother posting due to it being covered. I don't post up every time I get something replaced under warranty because.... well... what's the point? I mean if it's topical, sure but just starting a post to say "Telsa replaced my driver's side door handle under warranty today" seems kind of pointless.
I also haven't done a deep dive because I haven't experienced the issue but from what I've read it seems as though you need to pull your MCU (lots of videos available and sound relatively painless if you're handy) and then physically ship it to someone to repair. It seems as though turn-around times are around a week with transit and what not.
Sure it's not ideal but if I'm out of warranty I'm glad this option exists. I'd pay thousands to Tesla and be out a car at least a month as fast as our service centers are in this area. Not to mention I'd have to suffer the brain damage of trying to communicate with our local service center. No thanks.
While I think this was scary when it first start cropping up it seems as though the repair now isn't the worst thing ever. There's far more expensive items that can fail out-of-warranty in reality.
Not to mention the MCU1 cars have been around long enough to not only know what the common failure is but also have a repair in place. Time will tell what the weak link will be on the MCU2 or what it might cost to repair or if there will even be an aftermarket solution anytime soon.
Again, I'm not saying that I see ZERO benefit of the MCU2. That's not the case. There's obvious performance benefits. I'm just debating that the cars the MCU2 come in are worth the added buy-in that some around these parts preach about in some threads. Hell, if the MCU2 upgrade path ever arrives (might be accelerated over this eMMC issue if it ever hits Tesla financially) maybe I'll have a solution for a couple of grand to just upgrade it through Tesla when mine craps out. If they won't, I'm sure the aftermarket will since there's an untapped market.
tldr; I don't see the eMMC issue being such a big deal that a $20-25k more expensive car makes up that gap in "peace of mind" over getting a new MCU2.