Package re-installed "startup packages configure"

I have a need to install customized kernel package set (the usual linux-modules-<ver>.deb, linux-modules-extra-<ver>.deb, linux-headers-<ver>.deb, linux-image-<ver>.deb...). I install it on Ubuntu Bionic (18.04.6). It installs and things look normal, but once I reboot the VM, I see that the packages from upstream would have got installed (overwriting mine)!! I see in /var/log/dpkg.log, logs like:

startup archives unpack

...

startup packages configure

I thought that this could have been cached and tried to clear /var/cache/apt/archives, but still the packages are overridden! Also, before a reboot, when I checked all the packages were in ii state, so its not like any of them were in bad state and needed a re-install!

I am not sure why this is happening! Can anyone throw some light on this startup package install please? I just want to make sure that my customized packages override the ones from upstream.