Thanks for the interesting test results @Mad-Hatter.
So your Legacy save basically has it working as you would expect. It appears to function as it would prior to saves created since NEXT.
Your Permadeath save appears to function as it would with saves created since NEXT, with the Beyond bug included.
I had done extensive tests with a new save back in December 2019 (Beyond). Only planet side bases would store resources after deletion. While not being able to access the Salvage Module on a Freighter at all. I never thought of testing older saves.
So it appears to matter when a save was created or possibly when the BSC was placed for the Base Storage Capsules to function correctly or not? Perhaps it matters if you have a freighter from pre-NEXT or later?
Interesting to note is the fact there are in fact 2 inventories created in the save file;
These store the contents of the Base Salvage Capsules and are apparently for planetary bases and freighter bases respectively.
Where I assumed losing freighter base resources was intended behaviour, I am now almost convinced this is just bugged with saves created since NEXT. We should report this and not simply accept the fact that getting a new freighter makes you lose what you had built in your previous one.