True. Shirt sales impact mostly your bargaining power in negociating with your kit manufacturer and ofc the sponsors.
What is interesting here is City was considering changing their main sponsor deal. Since those deals are almost always longer than the 2 year contract supposedly offered to Messi, you would recoup some money.
And let's be honest, City is not buying Messi to recoup the money but to try and be even more successful.
It is Messi. If he asks for that clause, you give it to him. The older he gets, the less likely other teams will try to poach him anyway.
As you said, you managed to keep Guardiola longer than Bayern Munich. If you are competitive (and you are), Messi has no reason to leave.