I'm not sure if, by "the federation that Mastadon is using", you mean the concept of federation (in which case, I agree) or Mastadon's specific flavor of it; but, if you mean the latter, I want to say that's just a fundamental property of the concept of federated systems (as opposed to distributed ones): e-mail is also federated, and "where you connect" is the hostname on your e-mail server... if Gmail shuts down, so to will all of the connected links of people who decided to use Gmail as their host instead of running their own. I use saurik@saurik.com for my e-mail address, and (if I were to use Mastadon) would presumably also set up my own Mastadon setup, so I wouldn't be reliant on a large Mastadon host.
(Not said enough, though, is that DNS is itself federated: .com could one day decide to shut down, or simply take away saurik.com from me for whatever reason. Given the tradeoffs involved, I feel like that's the best place for me to stake my claim--particularly as custom TLDs didn't even exist back in the late 90s, but even now with them there are too many dangerous-seeming restrictions and the cost is too high that I'd still go with a .com--and yet it means that I'm not in some ways fundamentally different than the people who attach their identities to Google, even if I would claim Google isn't trustworthy, as that's just my opinion. I will say that gmail.com is also reliant on .com, and so there is an argument of my solution being strictly better, and yet I can make counter-arguments involving Google's political influence and the such.)
The issue, though--and maybe this is what you are focusing on?--is that, as far as I've ever been able to tell (just from perusing these random conversations: I do not myself use Mastadon currently), there seem to be features of Mastadon that simply work better if you are using a large shared host (which, to me, is kind of a fundamental design trajectory of federated systems: to obtain better discoverability, security, and ease-of-use, people slowly centralize onto a handful of larger players and over time the protocol becomes corrupted or limited by these large players who want to collude "for the good of the user" rather than remaining limited by the shared protocol).