You're asking the system to install a package. System packages are available to all users. If the package is going to work for all users, its dependencies also need to be available to all users. This naturally leads to what you're seeing: the system will not consider software installed only for your user, so it'll end up installing the same dependency system-wide that you had installed in your home directory. While I understand your frustration, I can't immediately think of a better way to handle this.

What are you complaining about exactly? That your package manager doesn't automatically know you've installed something manually?

Considering what you get for 1G it is worth it for most users. I would guess that you aren't the target audience for it if you're that concerned over space. 1G of space these days is nothing unless you're using an older system. It's just sitting on your disk and that takes nothing away from you if you aren't loading it. It handles 10s of file types and that requires a lot of libraries

In Ubuntu and Debian the dependency from pandoc to texlive is of the "suggests" type, not "required". So you do not have to install texlive to use pandoc. You may use an interactive front-end like aptitude and simply deselect all the suggested dependencies you don't care about (or configure aptitude not to install suggested deps by default).

I think these packages contains pdf as well which makes the whole texlive installation over 1gb. Even without pdf, texlive is pretty big. I don't think there is a way around it. You can use a docker image to isolate pandoc from the system.