This means that up to the point of viewing the settings file, for the specific vault the filename length limit still needs to bee determined (aka up to this point the vault was not unlocked).
If I look into our code, it is only overwritten if the value is set to -1 for a vault, see those lines in our code base.
It may be overwritten if your settings file contains errors (e.g. due to manual editing), because Cryptomator then falls back to a default settings file. Otherwise i cannot image how it is overwritten.
I don’t understand in your setup why you expect errors on PopOS, on most systems one hardly reaches the standard path and filename length limits. In this post i made a small example how to calculate the optimal file name length limit if you know the restrictions of the underlying filesystem.