What exactly do you mean -- when are they overwritten? During character creation, or at runtime?
For miniMAXIme, I've followed two premises:
- Character mods should be free to define new characters as the author sees fit.
- Changes to the main character made by third-party mods regarding invisible traits (maximum health, running speed, inventory size etc.) should be respected unless they interfere with what the author of the character mod envisioned for a specific character.
Reasoning: If I'm a player and have installed a mod that will give me a bigger inventory or unlimited building reach, I want to get that always, regardless of what my character looks like.
Therefore, the character mods I've control of (I, Robot + Among Us Character) create their characters in such a way that they store any traits that must be changed (name, localization, corpse, graphics, sound) in a table. They then make a copy of the default character and change all the stored values. In the final data stage, they either copy the values of all traits stored in the table to the default character (if no character selector mod is active), or copy all traits that are NOT stored in the table from the default character to the new one (if there is a character selector mod).
I've used "I, Robot" and "Among Us" as my personal playground where I can experiment with the interaction of character mods and my own character selector mod. Of course, I encourage authors of character mods to use these mods as a template, and "bikini swimsuit miku" does just that.
So, if there is any value that should not be changed by third-party mods, it has to be added to the table.
(By the way, there's another reason why I think this approach is better: Characters have a lot of properties. It's far easier to only change the things that do not use the default values -- it's less bloat, and more convenient for debugging.)
I hope this explanation really addresses your problem. If I didn't get your meaning correctly, please feel free to ask again! :-)