To be honest, I'm not sure what exactly the intended way is. I'm finishing my first build too. (SKR Pico FTW! :) )
I couldn't find a definitive answer to what to align to machine coordinates.
If you have multiple nozzles then those must have different offsets, so maybe the head camera is better at 0,0 offset. In my current setup I have my one and only nozzle at 0,0 and my top camera is at an offset. I found this to be easier to track with visual homing and nozzle tip auto changer setup, but I don't think it really matters as long as you're aware what is what and where.
When you home the machine and set the zero location to 0,0 that refers to the machine coordinate. That is arbitrary. Whatever is at whichever location at the moment your home switches are triggered means 0,0.
Since your camera location can be more easily matched to a physical location (it is where your top camera is looking) you can determine that is where your machine 0,0 actually is in the real world. If your cam offset is -25,-34 then this means that your machine location is +25,+34 from the point the camera is looking at.
The nozzle location derives similarly.
What helped for me is to think in terms of the fixed frame of the machine and imagine coordinates of the table. E.g. the middle of my table is 100,100 and I want the cam to show up right above it, then with your offsets the machine coordinates will read 125,134, but that is irrelevant as long as the camera is looking at where it should be.
Don't quote me on this though. Others might have a better method, or even some sort of official explanation. If I remember correctly there is a wiki article on coordinate systems, but I found it only moderately helpful.
Btw if you didn't know above the jog controls you can select your frame of reference and based on that the DRO will display camera or head coordinates.