In theory, your theme should have access to the comments number now. The plugin filters the value returned by the wordpress comments_number function. This is how it looks with the twentysixteen theme:
But the plugin is not filtering the value returned by the get_comments_number function. This is the function that returns the comment number as an integer (instead of a string like ‘2 Replies’). If you are not seeing a comments number where you expect one, this is probably why. It’s a little tricky, because that number is used to keep track of the number of WordPress comments as opposed to the comments generated on Discourse, but it should definitely get fixed. I’ll look at it asap.
I don’t know, but the plugin’s comment html can be overwritten in your theme. It wouldn’t be very difficult to match a theme’s comment styles. I’ll look into that soon.