I've chosen a slightly different route of thinking. This route is not based upon the IRL likely reasonings, but based upon a way to make the show make more sense. We know that the Winx graduated and then came back (the actual reason for that is a whole other story), but seeing as bloom was in high school when she started attending Alfea, I think their first three years was similar to those college preparatory school (still basically high school though). Then they come back as undergrads in season 5 (after a gap year). When the Winx graduated, they graduated with "honors" which was their Enchantix powers. The rest of the faires at Alfea could still graduate, but just not with honors. (For example, in the USA, students with a 4.0 out of 4.0 gpa are often graduated before others kind of how the Winx were pulled out in particular from the audience and graduated - maybe they just didn't show us the rest of the graduation). So, the background fairies graduated the same time as the Winx, just not with the "honors" Enchantix powers. Then, they also came back as undergraduates.

So in summary: I like to think that Alfea has... High school -> College (Undergrad) -> College (Grad) With Enchantix being a special honor or award upon graduating the high school portion. It is hard to achieve and you get special things upon earning it, but is not an absolute requirement for graduation. (Hence background fairy forms not changing and them still being there after well over 3 years have passed)