Your hunch is probably correct that "magic" attacks actually denotes what we would more commonly know as "special" attacks.
or more that it includes special attacks?

Like your Quake 3 example, i'd wager it can be parried as whilst the cast is "magic", the hit is physical since... well its an "earthquake" type thing, and i [personally] would call that a Special attack.
So it can be parried as its not pure magic, like say an enemy cast of Fire IV, but its classes as a "magic" attack since there is either an element of magic within its .... creation? process? .. casting i guess, and/or its not physically performed by the caster [like titans stomps]

at least thats what i guess is the case, we know and recognise a 3 type system; Magic, Physical, Special; whereas the game only has 2, which in turn adopts the 3rd into itself.

idk

official responce/clarification would be nice on this