Overwriting policy in upgrading

[Takeshi NISHIMURA]

https://wiki.shibboleth.net/confluence/display/IDP30/Upgrading says:
> The upgrade process is designed to be very safe, and will never overwrite any configuration files, views/templates, properties, etc. that you have modified, except ...

I saw the upgrade process never overwriting unmodified configuration files too, e.g. services.xml.

Is it intended? Isn't it safe to overwrite such files mechanically?

Sincerely,
Takeshi