This is IMHO the most backwards logic ever. Everything about dpkg and apt makes this process easy, from running an internal custom packages repository, through to "apt-get source" for any system package on a moment's notice, through to having everything just magically revert back to Debian-patched versions as part of the normal upgrade process assuming you versioned your custom packages carefully.

A well run Debian shop is a thing to be seen, unfortunately it's not cohesively documented in any one location on the Internet. If there's any problem encountered in the wild on the Internet, after 22 years, there is almost certainly a solid process built into Debian to handle it.

Compare that to home directories full of tarballs of binaries with dubious compiler settings and godknows what else, I have no idea why someone would advocate against it, assuming of course they've actually done sysadmin anywhere aside from the comfort of an armchair