The counter to that—and no doubt a factor for many like Slack—is that when you use a custom protocol/API you get to control the whole experience. You don't have to deal with bugs in third-party clients, wait for clients to get emoji support, and can control the look-and-feel (many of the Jabber apps I've seen aren't great).

This is obviously not ideal for everyone, but I suspect that outside of tech that using a custom client is possibly even a plus.