Honestly, I think one of the main reasons these tools are cloud-based is that they're easier to monetize. Programmers are really into hacking, and it's hard to earn any real income from the tools you develop.
Pay-per-seat works well when no proper competition to go against it. What we built with http://voiden.md should be free forever, with monetization on plugins, but only the ones that introduce costs to the team.
The blessing was that the team was already profitable on another tool, and VC-independent, so nobody shoved some dumb design decisions down anyone's throat.