The weapons compatibility config is set via the techcompat.cfg file in the /exe/flhook folder. Server side only of course. If you're running your own server, you can modify this file as you see fit. If you need help with that, ask on the DiscoveryGC forum, help section.
As for the playerbase - yea, it does that when you are missing some part of the cargo, or don't use the base deployment command properly. Check base.cfg (same folder) to see the exact amounts of cargo needed. Extra cargo is allright, but you need at least the values defined (you can modify that too if you want it to be easier to deploy bases - just set the only required commodity to basic alloys).
aeternus
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