Your general point is solid, but one quibble with the numbers - even the pricing page has an "enterprise" tier "for very large businesses".
There's no way a company with 5000 Slack users is paying the sticker price per head - they'll call Slack's enterprise sales team and negotiate some volume discount with whatever shiny enterprise-grade features, SLAs, support guarantees, etc. they need.
Adding to other large company problems, these people will need management layers, the team will need a charter for growth. Who wants to be the maintainer of the Mattermost servers in a large company? Add all of this up and then the slack deal starts to look reasonable.
Edit: Just to add some real numbers, slack costs $12.50 per user per month [1] - that is ~$750k per year for 5000 users = 5 engineers. (More like 3 really in the Bay area)
[1] https://slack.com/pricing