For the 80-100% throttle, There isn't much but there is a difference. Knowing RPM would definitely be helpful. Maybe worth investing in a tiny tach for the future. In my experience the difference is 6700- to slowly climbing up to 6950 rpm
The 2003 GTI LE base model means that it has a 717 engine not the 787. Which is why we have the confusion of having a water regulator or not. In this case we do not have one by design.
Using an older normal scantool you should be able to see the hours on it and even reset the maintenance hours to know how long you've been running the new engine. Maybe they were using something newer and more sophisticated that isn't backwards compatible? No idea there, but the older scanners could read up to 2003. At least it worked with last key I did on an 03.
The only things left that I think could cause a top speed or top end power decrease would be the compression or possibly engine to pump alignment or retarded ignition timing. ( I think having 145psi is a bit low for new or rebuilt. I tend to see 150-155 depending on attention to detail) I wonder if the squish is in spec or if the compression has in fact been lowered by the re-manufacturer. Did they use a thick 6 hole base gasket or size it up for what's needed. Whats in there for parts, OEM or aftermarket. Those are the things I wonder and question the overall build of the engine.
Another thing would be running lean on top end if the fuel pump couldn't keep up with demand or if there is a slight air leak in the fuel supply line. (I've only had one 717 engine do this 80-100% no change thing and it was the water seperator gasket leaking)
Try a plug chop at 80% and another at 100% with new plugs and See if there is a difference.
If the engine is performing to its max and the plugs are right, that could just mean its what that engine can produce.
Well that's all I can come up with.