Is arrival tax charged in airline ticket connected to passport used at check in?

Just a random question I was thinking of. I dont know how connected things are but a lot of countries have arrival tax charged via flight tickets. Would checking in with airline with one passport and then using another to enter a country cause problems? Especially now that egates are so common.

I assume there has to be some prior knowledge, data sharing and uploading of information onto these egate systems of who and on what passport people are arriving on. Maybe some prior authorization.

Having two passports and attempting to enter on a passport different than the one used with airline now cause problems? Could you technically be denied entry into a country using one passport and not another because an arrival tax wasnt paid? Assuming both passports allow visa free entry to arriving country.