For what it's worth, you are not the first to ask about this. Either my explanation on the Tests & Checks page in the booklet isn't clear enough, or Fudge dice have really gone out of style!
The key thing to understand about Fudge dice is that you are not calculating a number to determine the outcome; there is no DC and bonuses are not numerical -- it is a much simpler bell curve of success / fail / other.
Trainer bonuses are, in essence, another dice in the pool. Let's say you're doing a Smarts check. If you roll two fudge dice, and you get ++, that's a Super Effective Success on its own. If you have a single + bonus on it, that makes the roll +++, which is still Super Effective. So yes, to your question, if you are a Scientist with ++++, and roll --, it is still just Super Effective. It is up to the table to add flavor on the fact that you still over-succeeded despite messing up. But all that's need to truly "Pass", is one + (after all dice are combined). You are trading worse odds on all Charisma and Brawn rolls, and passing up other Bonuses, to ensure Smarts are always your time to shine for the character you want to role play.
What I don't think I mention, but preeeeettty sure I did on the podcast, and is standard in most TTRPG's, is that the GM can always make difficulty adjustments if necessary. So if you're rolling Smarts on a check that might solve an impossible fusion energy related equation on a chalkboard, and it feels very anticlimactic to just let the Scientist automatically succeed, the GM can add a - to the check. If you are injured, and normally your Swiftness is neutral, but last session you broke your leg, the GM might say all Swiftness checks for that player get a - while you heal.
Yes, this approach requires a good, free flowing GM who is not a dick. Some players and GM's really prefer more rules and statistics, because tactical fairness is an important part of the experience. But for me the place for that here is in the Pokemon Battles.
So, to your other question, yes -- natures, abilities, IVs and EVs were all left to their defaults in Pokemon Showdown or picked by the players. I noticed that the vast majority of people who play Pokemon can and will ignore these systems entirely and still enjoy the experience, myself included. So it's optional flair/management. Again, depends on the level of tactics that is important to your unique table of gamers.
I would take a look at this Expanded Rule Set if that's your jam. Super cool.
Levels are covered on the Leveling section; in 20 Sided Stories we started at level 5 and used a d4 in between episodes/encounters. I would then adjust the possible upcoming trainer and wild battles to what felt fair or interesting for the current party; normally the same levels, some a little lower, some a little higher.
Sorry for the essay, but this page gets a lot of hits per day now. So hope that helps you and future trainers passing through!