Decentralised and open source social network.
This may be obvious and not what you want to do, but Lemmy's own UI is optimized for threaded conversations within a post. Browsing Lemmy communities from an account on a Lemmy instance looks pretty sensible.
That doesn't help you manage comment toots from Mastodon, but if you don't find another solution... it will look better from Lemmy itself.
Although it's possible to follow Lemmy's communities in Mastodon, I would not suggest it as the experience is not the same. That's my reason to have separate accounts.
If you only want to be "notified" of new posts in a given community, I think you can subscribe to some sort of RSS feed. In Calckey (now Firefish), you can add timelines that will show specific RSSs.