Sure. You install your DE first, and then start installing software like browsers, email, etc. The net install disk is just a barebones system to get you up and running and then you install whatever you need from there. If you’re building a desktop them you might want a DE. If you’re building a server then you might want web or email services. The basic installation can be expended to include everything you want for that particular machine.
The advantage of using a pre-configured full setup is that you don’t need to know the name of all the packages you want to install, and typically you can still remove the ones you don’t like. Even with the DE you will probably find that the package also installs a number of common tools like task bar widgets or file managers. So in making a truly custom system you will have to hit google quite a bit to find the things you want to install, but then you learn what all those various packages actually do. Even the GUI login screen has multiple choices to select from which give you different ways of managing the logins. That’s one of the things most people really enjoy about linux – almost every type of software has multiple choices (like Firefox vs Chrome) so it’s easy to build up a desktop that suits your particular needs.