I think you didn't understand what I mean about they didn't cross.
I mean even if they actually meet similar event (fight with same demon, do same business), but those event not happen 100% same to other route.
In main route (assume this is canon storyline), Yuri must defeat Gildoll right at his first appear, else he'll escape and they discovered how to trap Yuri, she'll never able defeat him by herself, and Suzune never appear to help her.
If Yuri defeat Gildoll right at his first appear, that'll lead to Mekiden attack (if Gildoll alive then she won't appear).
But in Suzune route, if she obey Kanemichi, you can see Yuri somehow still virgin until the end, which mean she managed to defeat Gildoll by herself, however Mekiden never appear even though Gildoll died, which not happen in main route.
If she disobey Kanemichi, later she'll come to help Yuri defeat Gildoll, I repeat this never happen in the main route.
Which mean, if you pick the main route, then entire Suzune route become non-canon, she might somehow escaped Kanemichi, cure the president, but you can't guarantee she still virgin (for example, she might agree to have sex at first, but then she recognize he's just lying, cause him insane, then ask the goddess to cure the president, come to help in Mekiden incident). As I said before, it's up to player to decide the sub girls fate because you don't actually know what happen with them.