So frustrating for you but I think there may be error on Isabella's parents' names as reported by informant to her death

Does happen and a pain when it does, particularly in this case, when she seems to have used a number of surnames for her registrations.
Not sure whether trying to source her marriage cert would help? Were parents' details included on these certs for the period when Isabella and Alexander married? Her marriage cert would at least include info that Isabella herself had given.
Everything is pointing to that birth that Ev found earlier. Location, year, and surnames that Isabella went on to use in later years in a number of combinations. The name given for her mother on her DC seems to be a combination of her grandmother and mother's first names:
Looking at the IGI -
Isabella Miller Thomson born 11th sept. 1860 Leslie Fife
mother Townsend Thomson
Monica