I cannot address your specific warnings, but I do know that when you run System updaters the installation process requires that the Installer "take over" your computer. To do this requires modifying permissions on certain System files. Once the installation is complete you get back your computer, but Disk Utility may note that a modification has taken place.

I have seen similar warnings myself on occasion, but not to the extent that you are currently.

On a Mac since 1984.
Currently: 24" M1 iMac, M2 Pro Mac mini with 27" BenQ monitor, M2 Macbook Air, MacOS 14.x; iPhones, iPods (yes, still) and iPads.