Most things depend on libc and you probably already have it installed.
On a debian-based system, Everything is tracked by dpkg, including dpkg itself and and very low-level dependencies. Therefore, if you're installing everything from a distro anyways, just start with that distro and replace the kernel if that's something you're trying to do.
When you use apt to install packages, you'll run into dependency problems if you're not installing all software from the same version of the same distro. Debian stretch has many incompatibilities with Debian buster and Ubuntu bionic. Where do you want that to be? Ubuntu's archive? Debian's archive? Elementary's archive? You'll also need to know which version of things to download. If you do use apt, you'll end up downloading packages from somewhere. If you and using a from-scratch system because you want a custom kernel, then you can install that kernel a debian-based system. I recommend using the same distro instead of your own "from-scratch" system. If your professor is using apt, then she is using a debian-based system.
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