I thought a bit about the logistics, and it seems to me like you want to make the 2nd and 3rd boosters first, then shuffle in all the alpha cards and construct the 1st boosters. That way you minimize the required amount of shuffling and card sorting.
As for the mechanic, I think it's a good way to seed build around in the first booster, which means you could probably put this mechanic on even more cards than just six. I think I would use a sticker to denote the alpha cards, rather than print proxies, but your cube is already filled to the brim with proxies, so it's probably okay. If I were to use proxies, I'ld probably make Alpha a supertype, and put reminder text in the text box, so you can also alpha up (legendary) creatures, where there's not enough space to put the explanation on the type line. So, for example, Approach of the Second Sun would be an Alpha Sorcery, and the first line of the text box would read:
(Alpha cards only appear in pack one.)
Good candidates for alpha treatment in my mind would be:
Though Braids is a good example of the problems you run into when you want to alpha up legendary creatures. There's no more room on the type line, and even adding just Alpha is going to make the line feel cramped.
I'ld be tempted to put these in an alternate border, to make them stand out both to the drafters, and to yourself so you can more easily remove them from the card pool after the draft.