One last info for those who are interested, what the devs intended:
I found on the dumpshock forum a thread from 2010 "Visibility Modifiers and SpellCasting" by searching for "+visibility +spellcasting +cover". Don't know, if I'm allowed to post links here, so I won't.
In it Synner, who was a developer of SR4A, explains about visibility, cover and why the change was made to make cover a bonus (in SR4 it was a penalty).
It was because attacker very often "forgot" to apply the cover penalty of the defender to their attack and spellcasting rolls. The devs thought, that it would be very rare, that the defender would forget to apply a cover bonus to their own roll, so they put it there.
I won't say more about, what this thread says about cover and visibility. Everybody can decide for themselves, if they are interested, in what was intended and if he wants to read it or not.
I have no problem if people play with other rules than me, if it works for them. I just tried to be helpful by finding quotes that would clarify the issue and I will stop now.