OP referenced Trollskull Manor, which is in Waterdeep Dragon Heist, a campaign that runs from levels 1 to 5. Without handouts or BSing rolls, it is not possible to have two ability scores be 20's and one be a 19 unless the player rolled three 18's. I'm not willing to believe that they did.

They could just be using the setting and not the module, but it remains the case that it's not possible to have those stats without rolling several 18's + ability score upgrades.

Also, yes, it's completely fair. My players don't roll for stats at all, and the few times I've had them roll for stats and such, I'll 100% check over results and make sure balance is correct. My players who roll very high like it just aa much as the ones who don't, if not moreso - they don't feel entitled to their scores, they care more about everybody else at the table having just as good a time as them, so an even footing is more important.