I used to worry about this at first, but I think I've made my peace with it.
The only real difference between this way of doing things and the conventional forum interface is that the latter can will only show you one updated discussion per forum in the default view. So in order to check the latest forums, you have to click a forum and wait for it to load; then go back to the top, click another forum and wait for that one to load; and so on, ad nauseam.
I've come to realize that I really didn't enjoy that process ... it's probably one of the main reasons I've never been a very avid forum user. With Flarum, at least, I get the latest updates without all that clicking. Granted, reloading the forum in the morning and seeing a ton of bold threads can be a bit, well, daunting. But I think it's better than knowing there are a ton of updated threads out there that I can't see without clicking around for them.
One way to alleviate your concerns might be to add a feature that's in esoTalk, but not in Flarum yet: the ability to mute tags that one isn't interested in, so they don't show up in the All Discussions list. I wonder if anyone has brought that feature up yet?