If you rely solely on the Motor Carriers Atlas you won't be seeing the country. Semi trucks don't typically travel on the scenic routes. In 16 years of full-timing and traveling constantly, we've never gotten caught on a road we shouldn't have and we traveled secondary roads 90% of the time. There are many, many roads that the Atlas says semis should not be on. It has nothing to do with low clearances. Sometimes there's a truck route bypassing a smaller town if they don't want semis driving through town. That has nothing to do with RVs.
If you travel west of the Mississippi you'll have no problems. We use a variety of resources - DeLorme mapping program, Garmin GPS and our favorite is the Benchmark series of individual western state road atlases. We also use the 'Mountain Directory' book. We've never used the Motor Carrier atlas. If we really have a question we'll Google that particular road but again, everyone we've planned we were able to go and we love mountain highways.