But what if the Advance quotas for Stockport have run out but there are still Manchester Advances available.
Given the way that advance quotas work, that's extemely unlikely: if the cheapest tier has gone to Stockport, it won't be available for Manchester either.
Ask the guard if you can get off early, if they say yes ask them to endorse the ticket. If they say no then see if you can buy a Manchester-Stockport single from them.
TOCs only really care when there's a clear intent to avoid a fare, Preston/Lancaster is the obvious current example for off-peak tickets. For advances, it tends to be where advances are sold to one station but not another (e.g. there are Megatrain tickets to Southampton Central but not Southampton Airport).