Yes, you are correct, there was a minor height differential between Omega Supreme and the other Combiners.
I could never tell exactly, since the scenes often had him fighting them, but from guesstimation, if a Combiner was standing looking at Omega, his head would be level with Omega's top chest plate.
That is the toy scale I am looking for.

I haven't seen the images of the upcoming SIEGE Omega with the Titans yet, but I know CW Devastator is the same height as that toy, so here's a sample to look at:
https://static.seibertron.com/images...722-033659.jpg
Omega Supreme should not be nearly as tall as a Titan!

The third party ones are even bigger, they are Titan size.

So naturally, I've never been convinced that either of these toys are the correct size, given they're invalidating the known scale chart completely!