I worked on the desktop client for several months up until the first public beta release.
No, Mailbox for Mac has been a fully native app since inception - which is how you get those nice fluid gestures.
What happened next I have no idea, since I left the company. If I have to guess, we incurred a lot of technical debts during the sprint to beta, and they were doing some major rewriting to fix them. Before it was finished, the project was axed. The new version was released nonetheless to support sunsetting.