If you play mutually exclusive scenes it kinda breaks the game. Some immediate flags are set or reset based on the decision, but other flags get set and stay set. Plus any RP points earned on the numerous routes are kept.
An example is, at the DIK party if you choose to go back to see Maya and the mc ends up fingering her, the "Finger Maya" flag is set which has an impact as far down as episode 6. If then, using the mod, you go back and choose to dance with Sage instead, it will clear the flag that indicates you chose Maya over the party, but it will still leave the fingered Maya flag.
I'm not going to go through and debug the entire mod, but it definitely has the potential to mangle the game. You may never realize it has happened though, since some times the effects of these flags are subtle, or something may end up being unlocked that should have been locked and you're none-the-wiser.
Hence why I'm not a fan of the walkthrough mod. It undermines the author's intentions just so completionists can see every scene. Of course everyone has the option to install the mod or not, but it's just not widely publicized as to some of the adverse effects.