Just an idea, don't know how feasible:
Say you finished an air factory. You want 1 bomber, 1 scout, and then your inties/scout loop. Imagine you could mark that first bomber as "exclude this from the loop" (e.g. by pushing Alt while clicking on it or something like that). The factory builds the entire queue once, then only loops the inties/scout going forward.
I often have the issue with my first land factory on a small map. I queue up four engies and two labs for initial expansion/raiding, but afterwards only want tanks, scouts and arty. With loop turned on, I may forget to come back and remove those engies/labs from the queue, and so at minute 3:00 I have an extra four brave engies and two labs facing off against six enemy tanks...