I agree. The Store is a new version of Livery, offering nothing new except the preview function. An obvious implementation would have the Livery upgraded to include the preview. There would be no new button in the station menu for us to complain about. The Store then would be a re-implementation of Livery that was intended to replace it. But the Store doesn't allow us to apply the things we buy to our ships.I'm ok with there being a store (though it's weird it is called that - as the shipyard etc are already stores). But previously in Livery you could see things you didn't own - and it took you to the website to buy them. The introduction of ARX could have simplified Livery so it just allowed you to buy if you have the ARX. So I don't know why there is also a Store link. And why the preview to see new things only works via the Store link, and is broken via Livery. Like they were scared of the Livery code so did the 'we'll just build a new version and stick it next door' coding method.
On the other hand, a clean implementation would put everything related to Arx on the main menu. A new Store would let you buy both ship packs and Holo-Me packs, and the in-game Livery and Holo-Me would allow you to apply the designs that you already owned. But the Store doesn't allow you to buy Holo-Me packs. Also it would mean that you couldn't spend Arx while you were playing; it would have reduced the opportunities to spend real money below what they already were. So it's easy to imagine that they decided to put the Store in the station menu so that the opportunities for spending were maintained.
Neither of these designs was completed. Livery still allows you to spend money and you can't apply paint or buy Holo-Me packs in the Store. It may be that the design changed part-way through development or it may just be that they ran out of development time. It's easy to imagine that they found themselves in bug-hell with the Arx changes in game-play bringing up issues throughout the game and it was all hands to the pumps to fix everything before release. (And they still missed two or three such bugs, out of the hundred that they might originally have had.)