'Refit" is a term used to say that the ship is "better than default". In the case of the Exploration Cruiser refit, you actually get a new ship configuration that's slightly more powerful than the Tier 4 Exploration Cruiser (better inertia, slightly better consoles and bridge stations) - essentially, the Exploration Cruiser Refit is like... Tier 4.5 : you can use it as soon as you are a Captain.

Whereas the 'Retrofit' is the term used to say that it's an older ship which was made so that it would be as powerful (relatively speaking) to the other ships of the same Tier. The Exploration Cruiser Retrofit is essentially an Exploration Cruiser which was balanced to have Tier 5 power which would have it be as viable endgame as other ships such as the Assault and Star Cruisers. You can only use it when you're a Vice Admiral.