There is no way TouchID will work if the sensor is replaced by anyone other than Apple. Moved to a new display? That will work fine, but new sensor? Nope.I feel they should still be running this check on every boot, not just when updating.
Otherwise you might get a 3rd-party to replace the sensor, they don't re-pair the components properly, and then some months later when you update TouchID suddenly stops working.
It would be better if it failed on first boot after the update, telling you that you need to re-pair in order to continue using TouchID.
Someone could however have been using the replaced sensor as a standard home button and then when they upgraded iOS it could have been bricked. In other words, if TouchID is operating you will not get this error.