Take a look at the sentence just two sentences before the mention of the cover modifiers (page 183, emphasis mine):
The target resists physical spells with Body and mana spells with Willpower. If the target is also protected by Counterspelling (p. 185), she may add Counterspelling dice to this resistance test. This Opposing dice pool is further modified by any positive cover modifier the target might benefit from (see Defender/Target has Partial Coveror Good Cover,p. 160).
The general explanation how effect of any spell is determined tells us it is resisted by Body or by Willpower. Every spell is modified by any cover modifier.
Do you think, that they would have wrote this about the cover modifier just to mention something that is only meant for indirect combat spells.
Technically you are right, the words "Defense roll" is very unfortunate and in my opinion is a result of this being written in the combat section.
I personally have no problem with giving cover modifiers to all spells, because I can well imagine that it is easier to establish the mystic link to an "aura" whose owner I can see completely than to an aura whose owner I can only see a small part of.
If I can establish the link without problems caused by cover why am I having problems with visibility (which is stated for all spells on page 183 second paragraph of "choose targets").
In case of visibility there is no way out (like the use of "defense roll" in the case of cover) of this general description of "choosing targets" for all spells.
By the way: do you give cover modifier to targets that are surprised?
Because by RAW they can't have one, because "Defender unaware of Attack" says there is no defense possible, so there is no defense roll, so no cover would count.
I would think it's not as easy to shoot a target that I can see only a small part of than its full figure, but by RAW it would make no difference because cover is only used with Defense dice.
Edit: Just saw that Noble Drake posted while I wrote with similar arguments, but not exactly the same, so I will leave the post as it is.