Throughout my "carrier" I tried to avoid mocking up EEPROM in FLASH at all costs exactly because of these issues... I even grabbed on the opportunity to use FRAMs at the very moment they appeared at the market (and used battery-backup RAM before that, although I admit that in the long run that can develop to be a major pain in the **** too).

But that might be because of the rather specific applications I had the opportunity to work on, requiring relatively frequent rewrite of a relatively large number of variables which needed to be preserved during powerdown. Would that be the relatively usual case of "only configuration data, seldom changed", I would probably go for the clumsy FLASH way, maybe maintaining two pages with a marker to indicate the fresher one (I do that with the batRAM/EEPROM/FRAM anyway); otherwise, if speed (granting the cost of FRAM) would not be an issue, I would insist on a different mcu or an external EEPROM (they cost practically nothing these days).

(There is one exception and it is the BASIC52 mod for AT89C51xD2/P89V51RD2, but that again is a rather specific case).

I know this does not help much, but I am afraid it is quite hard to surprise you with something you did not know before... ;-)

Jan