Let's say you decided to pick the Galaxy Refit instead of the Defiant Refit with that token, but then decided you wanted the Defiant-R as well. You'd have to earn a lot of Emblems in-game in order to buy it. Or - you can buy it once in the C-Store and have it permanently unlocked for all your characters, freeing up that ship token for one of the 2 other Refit ships.
Are emblems like exploration badges? Can you only get them at Admiral?
Essentially, yes. They are the current top-end (Vice Admiral) grind currency, earned via daily missions. They can be traded in for Mk XI gear, or exchanged for RAdm Marks (see below) if there's a particular Mk X item (e.g. Covariant [cap x3] shield) they want.
Rear Admirals get to grind Marks of Honor (PvP), Valor (STFs), and Exploration (guess) to trade in for very rare Mk X gear.