Travel times for transfers or expansions or proxies are pretty hard (virtually impossible) to do automatically, but I suppose the program could ask the player the distance the building is being built, and account for the loss of mining time accordingly. It hardly seems worth it considering the work involved though.
I don't know if this is intentional or not, but I happened to get a 1 second discrepancy (at only 1:41 into the game) by doing identical build orders.
The build order was extractor trick, 11 overlord, 10 pool, 10 drone.
However, the first time I ran the build, I messed around FIRST by canceling drones 4 times in a row (is that even possible?), an then undo-ed all my actions to the start then re-did the build.
I guess adding a "scout for x distance/time" would also be able to simulate building distance, but not-so-much transfers easily.