The drawback to this though was that the best are easily bored. FogBugz was an important cash cow for the company, but there were few truly novel problems to solve. This was not a "web scale" effort -- it was self-hosted software for tens to hundreds of seats.
So I speculate that they okay'ed the project just because it was an interesting thing to do that solved the underlying problem (albeit in a bit of a convoluted way). The simple cost/benefit analysis from a management point of view is simple; pros: your devs are happy and you get linux support; cons: it's a little more complicated and people make fun of you on the Internet.
Over time, Fog Creek came up with better outlets for this kind of nerd energy -- kiln was fun because there were mercurial nerds around; trello was a foray into server-side javascript. There was still a bit of that "the nerds rule" bad decision making that made FogCreek an awesome place to work, but it was more constrained.
Since then (and I'm way out of it now), a lot of the old school "just badass" programmers have kind of gone their own way and Fog Creek has hired folks who are better aligned with what they do and how they do it. I'm not sure if this is because of a masterful shift in recruiting philosophy or if the diminishing recruiting brand (due to Joel's blogging pause) led to the right kind of developers becoming interested naturally.
In either event, it was definitely a very interesting culture, and I'm happy to have been able to play along for a summer :)