I am on Mastodon, Peertube and also have a WriteAs (WriteFreely) account, they serve different purposes but federate, so Mastodon can follow the other two, and I think comments on my peertube videos made on Mastodon can be seen on Peertube.
I guess it is a little like the Unix philosophy where there is a tool that serves a specific purpose, but does it well, and all those tools work well with each other.
So not really a problem having multiple accounts across different purposes, as for different accounts on Mastodon, it may be harder to manager, but if you have different user accounts on your computer, it would make things a little easier I guess.