ReplyTool currently adds its reply links to signatures appearing in blockquote elements.
Among other things, this would impair the section identification in the planned topic notifications feature. As @matmarex has pointed out, the oldest comment in the section is planned to be used for section identification, and the quoted comment is quite likely to be the oldest in the section.
The other possible invalid signature container is the q element.
Convenient-Discussions also excludes elements with the classes defined in the wiki configuration, which is useful for process notes such as "This section has been moved from...", quotations that are for some reason not in blockquote tags (although it's better to make the quotation template in the wiki to use the semantically correct tag), and other cases. But that would require additional configuration.