Having ancestors from Germany and London, I can appreciate your headache.
Perhaps you could post a couple of examples where you are struggling.
I have Bermondsey, Southwark, Surrey; Bermondsey, Surrey and Bermondsey, London and places in Shoreditch suddenly becoming Hackney.
I guess the issue is that local government keeps changing - do you try to mirror that with the Sanitary, Rural or Urban District, Borough or District or stick to the often only Ceremonial County? I certainly know that Bermondsey is in London, but to me it makes senses to use the historical reference and then to note what is known as now (which could of course change again under some future reorganisation).
Some of my ancestors are from Lincolnshire and certainly the boundaries have changed, except for the Ceremonial County which crosses over into neighbouring areas. I've seen reference to North and North East Lincolnshire and also the smaller areas of Lincoln, North Kesteven, South Kesteven, South Holland, Boston, East Lindsey, and West Lindsey. Is it best to stay with Lincolnshire or to refer to the local government area for the time period looked at?