Starting bases aren't modular. If your ruleset specifies it, it completely clears the previous definitions. They're too complex to make "modular" as they contain savegame content, not static ruleset content. Stuff like crafts, facilities, items, etc, aren't unique and trying to merge them could cause really odd combinations and behavior. Plus it's really ambiguous. In your case, you could be trying to replace the existing starting items, or adding to the starting items, or trying to combine them, or...
The best I can do is add a workaround so for example specifying "items" only overrides the "items" of the startingBase instead of the whole thing, but any deeper and it gets hairy.