From a Toyota perspective, my friend is the head tech at a Lexus dealership. When we hooked up their tool to my 4Runner, there wasn't a whole lot that was able to be changed/adjusted that wouldn't readjust itself after a drive cycle.
Did we miss something?
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It's a Toyota thing, they really don't let you mess around with their vehicles even with a factory scantool. They are also really weird about features (for example a 2005~2015 Tacoma does not have the ability to use the scantool to add a remote key fob, yet any 4Runner does).
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In OBDII there's "Mode$06" which provides "PIDs" or "Parameter IDs". The easiest way to think of it is this way:
A DTC (Diagnostic Trouble Code) is the "failed" result of a test that the vehicle ran. i.e. I ran Test P0301 (Cylinder 1 Misfire Monitor Test) and the result failed expectations, so I set DTC P0301.
A PID (Parameter ID) is the actual test the vehicle ran, so if you used a Scantool to read Mode$06 data (I forget what the ID number for cylinder 1 misfire monitor is off the top of my head) you could see the results of the test the vehicle ran that lead to P0301. You could see that the vehicle wanted no more than 40 misfire events in 200 revolutions (arbitrary numbers here, so don't take them to heart) and it saw 56 misfire events.
OBDII provides some PIDs because it's federally mandated from a OBDII standpoint, but the manufacturer doesn't have to provide ALL PIDs to a generic OBDII Scantool, just what federal law requires for the OBDII standard. Everything else falls under "manufacturer specific" and that can be coded, visualized, and presented however the manufacturer wants. With a factory scantool you can see PIDs that a Generic OBDII tool will not and those can be useful for pinpointing specific issues and oddball issues, like say seeing how badly a Catalyst failed to see if it's "Borderline" or just shot.
Post Note-
I don't remember if I mentioned this in my Toolbox thread (should review/rewrite/update that at some point... X_x ) or my MIL thread, but if you want to really get good at diagnosing stuff; always assume the scantool and/or vehicle is lying to you. I know it seems counter-intuitive to say don't trust what the vehicle/scantool is telling you, but hear me out. A DTC is a failed test result of a test the ECU ran, that's it. The ECU ran a test, it got a result that failed, and it set the DTC; BUT that doesn't mean the test was accurate, the results were accurate, and/or the ECU is accurate. So if you approach it from the mindset of "the ECU
thinks it has a P0301, does it have an actual misfire in cylinder 1?" (then you would verify if it has a misfire, if not you'd try to figure out why the ECU thinks it has a misfire when it doesn't, ect.) it will save you a bit of a headache on some of the weirder issues. I've been guilty of this as well, I've taken the DTC at face value and spun around in circles because I was thinking "it says it has this problem, so it HAS To be THIS ISSUE" and it turned out it was something else feeding false information to the ECU giving it a false test result. This is why there's a misconception that people think just pulling DTCs when you have a check engine light is all the diagnosis you need and the tech is fleecing you for an hour of labor to pull code (it's almost never that easy.)