After oyu have read the mail you should be able to just go back to the keypad and then it should open up actually.
If this does nto happen , can you please send me your savegame file so i can have a look into this ?
The crashed APC does not have something to do with the pilot seat xD
These are two different things.
So what you want to do now is
1. open up the inventory and click on the quest which says that the key is under a pilot seat in a crashed fighter yet (this is optional)
2. Fast travel to Mayas base and when you search around a littkle bit in the desert area you may find a crashed fighter plane with the pilot seat an the keycard
3. with the keycard you can go back to the little pirate base and unlock the crew quarter
4. in one of the crew quarter rooms is the emergency opener for the crashed APC
5. go into the APC and inside of the APC you may also find a energy core which you can use the power the nomad module near Malias house and then download scematics for material gatrhering devices which leads to another quest xD
Hope this helps a bit
and.. a little map to help you out
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