For me, I think it is better to say “not as high” or you could say “smaller”. The use of “short” in this context doesn’t feel right to me.

Yes, you can. However, the "shortness" of mountains is not something we normally think of. We think of mountains as being "tall" or "high", and that is the reason we are more likely to compare them using "taller" or "higher". Linguistically and logically though, there is no reason not to say "shorter". So, it is indeed a wee bit better to say "not as high as Mont Blanc" because it compares the mountains in terms of a concept (height) that is normally associated with mountains. I know this doesn't make complete sense because "shortness" and "height" are really just two sides of the same coin. We tend though to stick with the familiar: mountains are "high" and one mountain is "higher" than another. You are, however, free to do as you please. Do not try hard to use the words that most people use. The language is yours. If you want to discuss mountains in terms of their shortness, go for it!