I think you are more likely as not just mistaking which gremlin fight it was. LIke you upgraded a different item than you recall.
All armies on the maps are static at the very least, and nothing 'scales'. If Rune usage could have possibly made a difference, it would only have been the makeup of the army you fought. Since Gremlin towers are based on the size of the defending force, that could have, in hypothesis, changed them.
I really don't think it's true though.
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