I remember those functions, they seem to be remnants of some past era of software rendering using GDI (or they might be hardware-accelerated and used to draw desktop controls, I'm not sure). I wouldn't use them especially if you want to learn how transformation matrices work, since they hide all of that. All you really need is a form to display the results on, and a 2D array of pixels to render to, but of course you can use them if you find they are helpful. But you can absolutely do 100% of the rendering and computations without using built-in functions. You can even make your own vector and matrix class and roll with that, and I feel this is important if you've never done it before and are interested in low-level rendering.
In Win32 there are some standard functions for example: SetWorldTransform, SetGrapicsMode, etc. and structs like XFORM.
Should I make any use of those functions and structs or should I rather make my own ones?
It's up to you how deep you want to go. If you want to build on Win32 GDI to create your software renderer, you can absolutely do that and it's still fun (though you'll have to deal with the API, and you might not find as many tutorials as you'd like), or if you prefer to do everything from scratch, that's fun too but be ready to do a lot of linear algebra math!
By the way, re-writing existing code is not useless. It's important if you want to learn. Nobody would tell a beginner not to code Pong because it's already been done! It's only bad to reinvent the wheel if you want to get stuff done quickly, like a game. But If you're doing it for fun or for experience, reinventing the wheel is the right thing to do.
EDIT: The GDI API seems to be limited to 2D, so you might not find much use for GDI beyond accelerated pixel manipulation. I could be wrong though.