Tbh, I think the reason why you check SR only once, but once per enemy affected, is due to ease of combat flow while still giving each person/enemy an individual chance to resist (to prevent cases of a singular high roll = everything is affected). Combat already takes a long time anyway, and there's no good reason to require 2, 3, or even 4 SR checks per affected target per every spell cast every time their SR increases from w/e source. While having multiple SR checks might be more realistic, it's simply not practical for progressing through combat in a timely matter. Because by the time you have SR, lots of PC's and enemies have SLA's and Spells flying around multiple times per combat, and combats would be unnecessarily inundated with d20 rolls; it would undoubtedly increase 3 hour combats to 4-6 hours to resolve.
And just think if the rules actually said "Each time a creature changes their SR, make a new SR check for all spells currently affecting them and any Ongoing spells they come in contact with after gaining a new SR" or something to that effect. Our forums would be loaded with topics like "What SR Homebrew/House Rules do you guys use to prevent 6 hour combats" and "Our combat vs. an Enemy with a Dispelling Weapon enchant just lasted 7 hours due to 5,000 SR checks, are we doing this right?"