Still give you everything. I started with a fresh game and did not need anything; I only unlocked tech in the anomaly once I was done with the expedition.
Well, I did hit one wall on Saturday. Was the part where you needed to explore deep. Instead of diving myself, I thought I'd portal to someone else's underground base. Well, yeah, there was no base. and I was under 1300 water with my ship next to me. Had to start a base to build a Nautilus so that I can get to the surface. Once there, I was stuffed as I could not summon my ship.
After some googling, I found that you can summon the ship from a skiff. Lucky I unlocked that earlier, else I would have been borked.
Edit. Got rid of my portable refinery early on the moment they gave you a backpack one so could not use that trick to summon a ship.