You're reading too much into it. Also, you've confused two items:
Astral Perception & Aura Assenssing
You don't need to "read auras" or make any roll at all to use astral perception - it's just like normal vision. You choose when to put it on, and you automatically see everything clearly in the astral plane. Trying to "read into" what you see for more information, is different and is called Aura assessing. By RAW, an invisible person in a pitch black room hidding in super thick smoke is clearly visible, with no roll, to anyone astrally perceiving.
"The next thing a magician must do when casting a spell is choose her target(s). A metahuman spellcaster can target anyone or anything she can see directly with her natural vision." SR 4A, Pg183
"A magician in the physical world can only cast spells on targets that are in the physical world. Similarly, a magician in astral space can only cast spells on targets that have an astral form (though the auras of things in the physical world can be seen, auras alone cannot be targeted). An astrally perceiving (or otherwise dual-natured) magician can cast spells on a target in either the physical world or in astral space. An astral target can only be affected by mana spells—even if the magician is in the physical world astrally perceiving—as it has no physical presence." SR 4A, Pg183
As the magician is astrally perceiving, he can choose to cast physical spells. Remember, astrally perceiving does not mean you cannnot see the "physical world" - not at all. Astral Perception is a "bonus", it is like an overlay of information on-top of what you can already see. Sometimes it it is too much information, which is why when astrally perceiving you get -2 to all physical NON-MAGICAL actions.
What this means, is the magician can astrally peceive an obscured, hidden, invisible, etc foe and cast a spell on them without any penalty as spell casting is a magical action and not subject to the penalty.
tldr; Astral Perception lets you cast physical or mana spells on anything you can perceive in the "physical world" without the -2 penalty.