While the Metaverse uses a protected dataset for the AI races, there's no checking of the player's custom race. To test this, I edited all standard races down to only hyperdrive tech, and built myself a uberpowered custom race via object edit (text editing the save file). When I started a new MV game, I found that the standard races were back to their completely unbalanced glory, but my ubercustom race still stood.
It looks like you need to add in a check for rule compliance on custom races, or get ready to start invalidating submissions on a regular basis.
Additionally, the changes I made to the custom race starting system (pq 15 main planet, etc) were still intact.
After finding this exploit, I attempted to start a new, non-MV game with my custom race against the nerfed standards. This time, when I get past the race setup screen, and hit the opponent selection screen, my race is changed to the humans. Hitting back returns me to the setup screen for the Vincani (my race). Going forward again keeps me human, and I'm the nerfed humans in the Sol system when the game starts.
At this point, I clicked on menu and exited to the main menu, as mentioned in a prior workaround post. I started a new game, and this time, my custom race carries through to the game.