The only reason you'll need a basic Vega ship is for Conquest battle or for challenge planets, which you're given the option to refund the amount of the armor purchased, after which you can go to any hangar other than in Vega to re-install at no cost. There is no need for Vega configurations.
Parsecs are what this update is all about. Even though they allow for other ship configurations, you're basically wasting your cryo if you're not using them on Drac r70 ships and Parsecs. Nobody in their right mind would keep a r45 ship unless there's some sort of requirement for missions/events, which currently there is not. Currently there isn't an option to downgrade your Methanoid ship to Deluvian armor, but there should be. It seems unfair that they would not allow this to happen, since after the update putting Methanoid armor on your ship would disqualify you from doing missions/CQ/Challenges.