The way I understand the Magic rules: when you take the Magician, Adept or Mystic Adept Quality, you start with a magic rating of 1. (It directly states this under the quality in the 20th anniversary, essentially 4th edition, Shadowrun handbook.) If you cyber during character creation for a mage, the cybering takes place "at the end of character creation." By this, I mean that you Magic rating and Maximum magic rating get reduced at the end of character creation.
By this logic, If you want a magic user who has 4 magic and cyber/bioware costing 0.5 essence, then you must first buy (with Build Points) 5 magic (40 BP) and then reduce both current magic rating and maximum magic rating by 1.
Likewise, if you spend 1.05 Essence on upgrades, then for magic purposes you have 4 Essence (even though it's actually 4.9, it rounds down to the nearest number.) and so you must buy 6 Magic (65 BP) and then reduce it by 2 points to 4 due to essence loss. The reason for this is that you are going to your natural maximum, so you must pay the same number of BP as anyone else, you don't get special treatment just because you chose to lower your essence, especially since the cybering can give you great advantages!
My latest Magician has exactly 5 essence and 5 Magic. I spent 65 BP on his magic rating to make it 6, then the essence loss lowered it to 5. I got level 4 cybereyes with Thermographic Vision, Flare Compensation, the works. I got an internal airtank, and I got Orthoskin rating 1. Because of this, I can drop a smoke grenade or a flashpak and still cast with almost no penalty (assuming the enemy is not using thermal damping), I can easily survive inhalation vector toxins, and I roll 14 dice to resist gunfire damage.
As you can see, the essence loss and extra spent BP balances out in the end, and you can have a really effective (practical) character.
This is how I interpret the rules. Obviously it differs from many other people, but hopefully it helps.
