Way to make a configuration struct stable across versions?

It's called functional update syntax. Note that it takes an arbitrary expression and isn't limited to Default::default(). It's not allowed when there are private fields or when non_exhaustive is in effect, as there may be invariants that need upheld which could be violated by just copying or moving the private fields.

If non_exhaustive is not in effect and there are no private fields, you don't have to use function update syntax (if you supply all the fields), which defeats your "add options in the future" goal. So while I too would like to see non_exhaustive be applicable with privacy scopes other than just crate, it wouldn't actually solve your use case on its own.

This would be some new "allow struct expression but require functional update syntax" feature in concert with non_exhaustive, or perhaps "require functional update syntax" in combination with all public and defaulted field values, etc. There's some related discussion in the future possibilities of the default field value RFC.