I would say once you get out of the instructing business and into airlines and such, that it probably doesn't mean squat. And it really doesn't mean that much while looking for CFI jobs either, except that some 141 schools want prospective employees to have 141 experience. I went to a 141 school, and am currently teaching a 141 syllabus under part 61. Like you said, the end result is the same, and the end result (plus the hours of course) is all most companies probably care about.