> The main problem I have is the fact that you are pretty tied in with your instance.
That is in fact emerging as a feature of Mastodon. While messages can and do propagate quite effectively, it takes much longer than Twitter and does so less reliably. This means instance choice has a very profound effect on both who you talk with and who you will reach.
It's still entirely possible to follow people on other instances, and it works fine. But it discourages certain types of use:
1. Advertisers: reach is much less predictable.
2. Spammers & trolls: While troll instances exist, they get blocked.
3. Bots. See above, it's painful & captcha-gated to open accounts on many instances.
Search in the context of microblogging frameworks like this has always been of questionable value, as ranking on recall is almost terrifyingly time-gated. This further damages the reach of any ONE message but allows for conversations as a whole to be somewhat observable (e.g, gaming vs #gameing).
> If, client-side, I just create a bot that auto-posts on multiple instances, if my followers on a given instance are following different versions of my account, the federated feed on that instance will be spammed with multiple posts.
I would advise not doing this, as we will start to block all your accounts. Attempting to chorus-spam the federated timeline will show up very quickly.
In summary: The slightly slower and less reliable delivery is a feature for human discourse at the expense of automated discourse. That is good, not bad.
It can be frustrating when you as a human have to maintain outsized attention on two or more locales. We can fix this client side (maybe) or we can solve this structurally. In effect, the community is preferring the later. There are many very small instances (even witches.town is pretty small) all arrayed around a few very central "hub" instances where most of the traffic originates from due to population.
You may track your hub account frequently but need to do much less work for spoke accounts.
The experiment of: "Your choice of primary identity and its location having consequences on your experience of the network" is fascinating. I have instances I am on only for the local timeline. I would not want them to mix with my more public account.