The thing to remember is that while the hitting tree and ballpark effects are linked, they are also separate.
So, first the determination is made as to whether it is a hit or an out (combining the batter, pitcher, and singles modifier), then if it is a hit, the type of hit is determined (combing the batter, pitcher, and XBH modifiers).
The dimension of the park determining how man lost HRs are turned into 2Bs, 3Bs, 1Bs, or outs is already included in the other modifiers. The Astrodome and Comerica, for example: At the Astrodome Those HRs are turned almost exclusively to outs and 2Bs, the out portion is reflected in the hit modifier at the beginning. At Comerica, the HRs are turned into other hits, most likely 1Bs an 3Bs...
The sim is taking "it" into effect, it just gets broken up into two different segments of the hitting tree rather than having the ballpark effects all lumped in at the same point.