At GitHub, we faced the same issue when ZenHub [1] came out with their chrome extension. While, Slack is well within their rights to _ask_ you not to modify their user experience, it's short sighted of them to do so. With ZenHub, we worked with them even closer because we saw that our users were happier using GitHub + ZenHub. We made it super clear that UI changes would likely break their app but that would be a risk…
Worth mentioning that github ended killing ZenHub, by introducing github projects, which is essentially copycat of the only useful feature ZenHub had.
GH projects also has this arbitrary distinction between notes and issues, and notes are more or less useless yet the default when adding new items to the board.