Logic might be assuming you can get back to your random starting location even without Mirai.exe if it's a backside start.

[Pokerific]

Spoilers.zip

Looking at step 3 of the playthrough, it puts the Ancient Chaos shop in logic, after having gotten the Claydoll Suit from the shuriken chest, even though there's no way to get back to it without either mirai.exe, or birth sigil and feather/grapple claw.

[mokesmoe]

According to the randomizer info the logic shouldn't even be able to go somewhere it can't get back from in the first place. I had an unbeatable seed with an AC start connecting to a dinosaur gate.

Spoilers.txt