I just want to emphasize ... that every opportunity exists for you to grenade a perfectly good motor.
While anything is theoretically possible, on a naturally aspirated engine, you'd have to work pretty hard to actually cause significant damage through tuning -- worst case you run poorly, stall, or get some pinging and start over. While I agree that it's important to work slowly & methodically, and I realize you disclaimed your post saying that you're not trying to be discouraging, but it sounds pretty discouraging.
Just to level-set, you probably wouldn't share the same cautionary advice with someone installing an AFPR or setting their base timing at the distributor. But the truth is, they can do just as much damage with either one of those as they can with the tuner.
I like this quoted from the Tweecer Getting Started guide:
While it is possible to damage your engine using a tuning product as
powerful as the TwEECer, it is far more difficult to do than some “Pro
Tuners” will lead you to believe. It is however, extremely easy to
make your car run like crap just by making a single change that is too
far from what is needed for your setup.
No one is going to add 20 degrees of spark advance and pick up 100 hp,
though it is a good way to cause physical damage to your engine. This
would be over time and you would have to ignore some pretty bad
detonation / pinging and probably less than stellar performance, for
the damage to occur to a naturally aspirated combo. A boosted or NOS
setup would be far more prone to quick damage in such a scenario.
This is not rocket science and is not all that different than turning
the distributor and changing jets on a carb, it’s just the electronic
version of it.
Now I will be a little discouraging and say that by itself, you're not going to get much of ANYTHING out of Tweecer or Quarterhorse. Ultimately you'll need to make mechanical changes which you can then fully enable through the tune. Maybe a tiny bit of extra spark here or there for 93 octane, and firming up the shifts on an automatic, but realistically you're not going to get much. It's still a really good opportunity to learn, however, when you're still stock and naturally aspirated. Once you bolt on a turbo or supercharger mistakes are a bit more costly.