They're separate purchases, with different special powers - for example, the T3 Nebula's console can be used on any ship, but the T5 Nebula's console (same buff but group wide instead of self only) can only be used on the ship it comes with.
They are separate purchases but if they come with any special skins, they should unlock that skin for all ships regardless of level. For instance, the three Tier IV +1 ships unlock the skins on the Tier 5 refits.
The Tier 4 Long Range Science Vessel Refit, Tactical Escort Refit, and Exploration Cruiser Refit all have skins that can be used on their tier 5 Retrofit counterparts. The Exploration cruisers can also be used on the Galaxy-X.
Also, all three of them as well as the tier 2 C-store ships and the tier 3 C-store escort have additional skins that unlock for their stock versions, but if you have the C-store version I don't think you'd ever bother with the stock one again.