I would think the only way to get the Limited Edition Alien pin with the 35th Aniversary art package is to buy the Alien LE pin, cabinet and all.
You can dress the FT SE/LE cabinet up to have the Alien LE game play experience by buying the extra pieces but the numbered plaque and exclusive 35th art package will only come with the whole complete Alien LE unit.
Same deal if you start with the Alien LE - you can buy the FT lighted ramp kit for the FT playfield but remain limited to just the FT SE art package.
Curiously, I have yet to really see pics of the FT SE and LE art package side by side.