I interpret the figurative use of the word "stomped" the same as I do for "wrecked" or "destroyed" or "annihilated". Basically, 'to beat easily/substantially'.
Do you have any examples of cases where it has been used to imply underhand behaviours? (Obviously if a SpaceX employee literally stomped on a competitor's prototype, that would be an example! But I assume that's not what you mean.)