To me this means that you just lose a point off of your current magic rating rather than your max magic rating is reduced by 1 per point of essence loss. If thats the case I'd imagine you can choose priority A magic for a full mage with a 4 magic rating, take 2 essence worth of cyberware, and then use starting karma and metahuman adjustment points to get magic rating back up to 4, or even up to 6. Is that right?
If you do the character creation steps in order, you would first assign your attribute points and adjustment points. That's the step where you raise your mages' Magic from 4 to 6. Then during the Magic/Resonance step, you'd give her 8 spells (2 spell per original magic point, before adjustment points are added). Then during the Buy Gear phase, you'd buy gear, reduce her Essence, and reduce her Magic at the same time. This is somewhat consistent with past editions, where your character's Essence rating functioned as a cap on their Magic/Resonance rating.
Now, some qualities allow you to start with a higher trait or skill - those only make sense if you can reallocate your attribute (or skill) points after you buy the quality. So obviously there are some exceptions to doing the character generation steps strictly in order. However, personally I would not allow a player to reallocate adjustment points to bring Magic back up to 6 after she had knocked her character's Magic down 2 points due to Essence loss in the 'buy gear' phase.
I'm not sure if, after character generation, Essence functions as a hard cap on your Magic score (i.e. not allowing you to raise it with karma as you earn it during play, assuming you are initiated). I don't think that's addressed in this edition, though I could be wrong.