The problem is that you have to wait for the patch to be bundled. I've watched that take a long time, while services I knew to be vulnerable had to sit there and be vulnerable because the organization deploying the service didn't have any infrastructure to apply a custom patch.
Consider the degenerate case, where you have to wait for a Debian patch because you paid for the research that found the vulnerability. More than one of my clients wound up in that situation. But that's not the only way to learn about a simple, critical source patch that won't land in a Debian patch for days.
$ apt-get source bash
$ cd bash*/
$ quilt new my_urgent_patch
$ patch -p1 < ~/my-urgent-patch.diff
$ quilt add file1 file2
$ quilt refresh
$ dpkg-buildpackage ...
$ dupload ../*.changes
# trigger apt-get upgrade on target machinesI know I'd personally chose maintaining the system packages and where possible put extraneous language dependencies in packages too (fpm comes in handy as it can deal with a variety of packages, gem, npm etc). It makes life a lot simpler when it comes to administering a bunch of systems and trying to keep things consistent.
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