It could be a problematic skill, but it is meant to model Hannibul Smith and McGyver all rolled into one - with a dash of Steve McQueen from the Great Escape thrown in. It is meant to model (I think) the person who can, when put in a tough situation, come up with surprising solutions often using available materials in an ad hoc or jury-rigged fashion. It isn't meant to represent the guy who can do a job as good as a specialist (JOT-4 does not make you both a brain surgeon and a competition grav racer....).
So, what could JOT levels mean and how could one intelligently (and in a balanced fashion) apply the skills?
1. A JOT level (even 0) covers 'an area' - be that automobiles, small arms, medical science, etc.
2. Each additional JOT level adds another 'area'.
3. In an area in which you have JOT coverage, if you don't have another skill which applies, JOT can give you an effective level of 0.
4. JOT also means you are generally very resourceful, and for each level, you should be allowed another attempt on a task that is not the kind where failing it once renders subsequent failures moot (you went boom or the window of opportunity passed). This does not apply at skill level 0.
So, in our example, with Scout Bob with JOT-2, Bob defines his areas as 'starship systems', 'atmospheric science' and 'xenomedicine'. So, if he hits a situation where he needs to make a skill roll associated with XT medicine, something related to atmosphere, or something generally related to starship systems where another skill doesn't particularly apply, he can take a shot at it with skill level 0. He can try a couple of times.
This makes JOT useful, a sign of resourcefulness, but also something not to replace normal skills. It also addresses the issue of multiple JOT levels .
In this case, Hannibul Smith and McGyver both have at least JOT-5.