After some parameter settings I was able to work at all (at least it seems like this) with the Arduino Yun board. It was frustrating to do it (I'm quite new and inexperienced) but if you're tenacious you can do all that you want.
Thinking some more about the lack of Yun support I have been wondering is it wrong to think of it as a general purpose Linux computer. Perhaps it would be more correct to see it as having a very limited subset of Linux capabilities which were/are not intended to be enhanced.
(from @Jantje) I really hope the Arduino core team fixes these issues soon (like in yesterday)
I haven't used a BeagleBoard or a Pi but the BeagleBoard website doesn't seem to contain warnings against upgrading the operating system.