(Author here) We have done several iterations to make it less annoying, well... As a developer myself, I am not a fan of the popover either.
While wearing the marketing hat, I would say intercom is useful to some extent. We probably won't have those customer conversations if we don't have that small bubble.
We are building a dev tool for database development workflow, which is not a big market. We are also based in Shanghai, thus unlike valley-based shops, we don't have many viable ways to engage (like private introduction, offline meetup).
Internally, we also struggle between the experience and the leads, and as this topic is raised up here again, it will surely bring up another round of team debate this week.