Interestingly enough, it looks like it’s designed to work that way. This is the relevant logic with readable names in place of the real code:
if ( "Show Existing WP Comments" is disabled or there's no Wordpress comments ) {
return only Discourse comments
} else {
return Discourse comments followed by Wordpress comments
}
Is think the “or there’s no Wordpress comments” part of the conditional could be safely removed if that would help you?
The number or timing of different types of comments won’t effect anything in a block theme as the each block is a contained element, so you get what you see.