No really anymore to explain so I'll rephrase the question: Does the chip damage from whirlpool influenced by weather or the ability water bubble which doubles the damage of water type moves?
NO they do not. The rain/water bubble only boost the power when you actually using the move, not when dealing overtime damage. Being trapped from a move like whirlpool, sand tomb, fire spin etc etc always deal the same chip damage regardless on weather or abilities that being 1⁄8. The only way to have trapping moves do more chip damage is if the Pokemon using the move holds a Binding Band, which is a held item to make trapping moves deal 1⁄6 of the Pokemon's max HP instead of the usual 1⁄8.
