Am I wrong in that some MTH and Lionel diesels (even in the supposedly scale ranges) tend to take a few liberties with the basic dimensions.
No, you are not wrong but there is not a set rule to how much MTH or Lionel models are off (dimension wise) or exactly how it differentiates from the prototype. You have to do the research for yourself because every model will have different inaccuracies. Also each one of us is different so it is up to you to decide which of the inaccuracies bother you. For me an incorrect paint scheme bothers me more than the model being off by a few scale inches. Most 2 rail guys don't care for the MTH or Lionel stuff due to the drive system. I have accepted their drive system because I don't see it ever changing (but it would be great if there was change like say a better gear ratio).
You did mention "scale ranges". The non scale lines of MTH and Lionel are usually WAY off and I would never even consider converting any of that to 2 rail. However there are exceptions. Some locomotives in the MTH Rail King line are scale sized as well as I have found a couple (not that many) locomotives in the non scale Lionel lines that were very close to scale size. The Lionel Camelback of about 20 years ago comes to mind. It has very little detail but the overall dimensions is close to scale size.
Are there any specific MTH/Lionel "scale models" in terms of modern diesels that are just so wrong it is not worth bothering to try to two-rail them or seek two-rail examples in the case of MTH ?
I am a steam guy so I can't answer that. I think most of the MTH and Lionel modern diesels look good but I don't follow or know those engines well so if something was incorrect I wouldn't know it. I do prefer the MTH engines due to the fixed pilots and full length handrails. All opinion.
I realize it is not your era but the Lionel GP30 is regarding as a very well done shell and you can buy a frame for it to convert it to 2 rail with a better drive system.