I think the writers like to take their characters, and their personalities and flip them on their head. Have an episode where Fluttershy sees something scary, then she has to overcome it. An episode where Twilight goes banana's because she hasn't solved a friendship problem...ya know, that kind of stuff. They put the audience in a familiar or uncomfortable situation, and set up many jokes surrounding it. In Big Mac's case, he wanted to be with Applebloom more, and the only way he really could have done that was to throw him into women's clothes. Uncomfortable scenario? Check. The familiarity with the audience comes from Applebloom's reactions to it all...honestly, if my brother was doing something like that to gain my affection and respect, I would feel pretty uncomfortable too. xD
The reason Big Mac became an Alicorn was merely for comedy, I wouldn't think too much of it.
The writers are smart, and know their audience well enough to put them in funny and familiar territory; that is all it is.