If I had used Muk & Alolan Muk GX's "Severe Poison" attack that places extra Poison damage counters and in the next turn use Koga's Trap, do they still place the extra Poison damage?
No, they don't. The new, normal Poison Special Condition replaces the old Severe Poison Special Condition.
Source: Unbroken Bonds FAQ (2019-04-19), TPCi Rules Team (2019-05-02)