I purchased Afterplace at the lowest tier, which only includes the Android APK. My fault for not reading things carefully.

Is there a way to pay the difference for the more expensive option and get the win/linux/mac versions, instead of buying Afterplace a second time? 

you unfortunately will have to get a refund by contacting customer support (which I am happy to grant), and then repurchase it. Itch doesn’t really have an alternative solution.