The park factor is based purely on runs scored, while the hit modifiers are rounded factors based on the relative number of each type of hit at this particular stadium.
So, for all we know, the actual numbers for each could be:
1B 2B 3B HR(l) HR(r) Park Factor
Coors: +2.50 +1.50 +2.50 +2.50 +3.50 1.37
Mile High: +3.49 +1.49 +4.49 +2.49 +1.49 1.43
But that still doesn't have an effect on the number of runs scored at each stadium relative to the league, which is how the park factor number is derived and would include things such as walks, sacrifices, and errors, that wouldn't be included in the hit modifiers.
Also, as far as I know, the park factor has no effect in the sim. It just serves as a gauge as to whether a stadium tends to be more or less pitcher/hitter friendly.