AFAIC, this "flaw" is caused by prefs.ini files which aren't reset between sessions since there is a tag field for relations in the [OpponentSetup] section.

Every time such scenario(s) would become active, the previous enviro settings are reloaded with diplo status for all corresponding slots/per Race and if any are re-used (for example, Terrans maintain *0* as their reference tagging) the code assumes prefs options *must or should* override the scenario conditions for that specific Race or any others.

Weirdly enough, that's exactly how i got the X-Worlds 05-A's Sectoid/X-Com & Aquatoid/Magnetic or Anthropod/Apocalypsion constantly initialized as Enemies at war from game starts (this strange situation being only within Sandbox mode & if slots remained matched from 0 to 12, though).