This is not minute. If all ranged attacks are ranged weapon attacks, then just say so. Alternatively, if all ranged attacks suffer in melee penalties, then just say so.
I don't know whether the writers want: 1) To subject non-ray ranged spells to in-melee penalties and allow spellcasters to use PBS and PS to overcoming the penalties; 2) To subject such spells to in-melee penalties and not allow spellcasters to overcome the penalties with PBS and PS; or 3) To not subject such spells to in-melee penalties making PBS and PS irrelevant.
All three possibility have rule-based and/or game-balance implications too big to ignore and yet they have gone ignored. This is not...
The rules already tell us that rays function like ranged weapon attacks. Ranged weapon attacks suffer in-melee penalties. Rays, therefore, suffer in-melee penalties. You can use the Precise Shot and Point Blank Shot feats for rays.
Acid Splash functions like rays, smells like rays, feels like rays, and tastes like rays. Why wouldn't the rules that apply to rays not apply to Acid Splash? If there are no rules that specifically state that Acid Splash doesn't work that way, there is no reason to assume that it doesn't.