I guess this is only of the issue that is so easy to solve on a
case-by-case basis (e.g. by setting a symbol property) that nobody has
bothered to write a general solution (e.g. by adding a keyword to
define-minor-mode that specifies what variables/user options to set when
enabled).
FWIW, I've been toying with the idea of adding a kind of "advice"
mechanism for variables.
Basically associate with every variable a base value and a list of
functions that modify it. Then minor modes can add a function to the
list (which would implicitly update the var's effective value) when
enabled and then remove it afterwards.
Stefan