Ye gods...
I have no idea why ranged Fortitude spells are potentially penalized and discipline spells aren't...except that I sorta get the idea of a mental attack not needing to to "aimed" while a "physical attacks" does. Personally I might have tried something along the lines of rays versus "emanations," with the first penalized and the second not. <shrug> I don't make the rules around here.
Thank the gods. I would mention that the number of attack spells that target fortitude is not huge (and diminish senses is sufficiently awesome to still be worth taking) so on a practical level I don't worry about it much.
There was a big discussion on the old (now lost) boards. This is the summary of our Stat Monkeys final clarification/position. I can confirm that there was/is a penalty for firing into melee with many spells. It does affect which spells I have selected with my two spell casting PCs.
I agree and concede the A:RPG book is unclear in its text on this point.