It's not a weird base, it's really the most natural base to choose, which is why it's called the natural logarithm. It doesn't particularly matter what base you choose, because you can always convert from one base to another, but often the natural logarithm is simpler to work with. For example, the derivative of ln(x) is just 1/x. The derivative of log10(x) is 1/(x*ln(10)).
This is because ln(x) is the inverse of e^x, which has the unique property that it is its own derivative.
I think this issue could be addressed on the front end.
The reason you would want a server that is federated with everything is so you can access all content at once instead of switching between accounts on different instances. If you could log into multiple instances at once with a single username and see content from both in the same feed it wouldn't matter if they are defederated. I think this federation thing ought to be, as far as possible, transparent to the end user.
The way this currently works feels odd to me - it doesn't really behave like a decentralised Reddit, because your account is tied to a specific instance and the content you see depends on which instance you pick. It feels like an awkward middle ground between a centralized service like Reddit and just having a completely separate forum site for each community.