Jack of all Trades will always "function" as a Skill-0 for you (so no "unskilled" -DM), regardless of whatever your J-o-T skill level is.
Your J-o-T skill level determines how many throws of the dice you get per attempt.
So with skill 1, you roll the dice once ... and that's your result.
With skill 2, you roll the dice twice ... and take the best result (what Pathfinder and a number of other systems would call "rolling at advantage").
With skill 3, you roll the dice three times ... and take the best result of those three throws.
And so on and so forth ...
See that this makes JOT a very powerful skill, as gives you retries and nullifies the negative DM for unskilled.
So, if you have a character with INT 8 and medic 2 (so, in MgT a doctor) and another with INT 12 and JOT 1, the second character would be better to try to diagnose someone than the Doctor, as he will have 2 rolls with a DM +2 (for INT), while the doctor will have only one roll with the same DM.
Likewise, having a +1 due to stats and JOT 1 but no Engoineering skill makes you better engineer than one having no stat DM and Engineering 2, as the second character must split his 2 levels of engineering among 5 specialties (so being skill 0 in most of them) and, even on those where he has skill, he has only one roll, against the 2 for the charaacter with no Engineering skill.
MgT treatment on JOT makes it already wuite powerful. It's true that if you have it at 4+ you lose skills, but having any skill at equivalent of 0 makes you a very powerful character, to the point of, IMHO, not being realistic.
The MT appreach (free retries), OTOH, is not only more balanced, but makes the skill also useful for fields where you have the skill (if you have Engineering 1, having a retry also helps you on related rolls). To limit its efects, through, as I have already commented in other relate dthreads, when I refereed MT I made the rerolls hazardous (more dangerous on failure), as it means using "unortodox" methods to achieve th results, so more possibilities, at the price of higher risk (using improvised tools may give you the edge, or ruin your drive)