We would determine which variables could actually have a problem.
1. Get the list of variables that use :set.
2. For each of those variables, see if it is used in any source file
other than the one that contains the defcustom. A script can do this.
Make a list of only those variables.
3. Now we have a much shorter list. We could use the whole of that
list.
4. Or we could check some of these variables by hand and see whether we
can prove some of them have no real problem. That could make the list
shorter.
5. After the init files, we add code to check each of those variables.
If the current value != the default, set the variable again to the same
value using customize-set-variable.