A while back I added a mode to webmention.js specifically so that I could show reply mentions as just being reactions that happened to have embedded text, rather than making them first-class conversational citizens on my site. I mostly did that because I personally didn't care for the way that long reply threads ended up looking, but it has the end effect of it just being a link with preview-popup text that goes to the original response, and it feels like a very nice middle ground.

I do definitely prefer people to comment natively on my site's comment system for a number of reasons, though, particularly because I really don't want people making public webmention-replies to my private/restricted entries.