Rationale: the application developers are using this option very liberally and also abuse it to force you to pay for some sort of "cloud" option. This is our phone, backups are protected and allowBackup should be taken as advice to user, not as something that creates huge issues if phone is reset for whatever reason.
Implications: I can only tell for me, but the only application for public bus transport that we use is requiring you to store some long ids and submit them to them by email to restore the account. If you lose them, you have lost all money that you had on account, the local bank requires you to physically go to their office to validate your id (an hour wasted), password manager (Enpass) forces you to either set up something like next cloud or sync your passwords with them (we all know how that went for Last Pass,...
Security implications: due to possibility that something will go wrong with the hardware or OS (don't take it personal, I am system developer for 25 years and sometimes something just happens) I am forced to keep bootloader unlocked so I can backup all the data using root. You would take a huge burden off my shoulders if the backup would actually backup all the data (for simplest possible implementation, there is an exclude list, pretick all the application that dont allow the backup, but allow to turn it off).
I am prepared to do it if there would be some agreement that such feature would be included into future updates. I am not really an android developer but I am prepared to figure out the code (would love some pointer where the backup code is) and implement possibility to override the allowBackup option.