Support Pokémon can boost a Magikarp's Jump Power 5-25% by cheering. This can allow a Magikarp to win a battle even if it would otherwise have a lower JP.
Can Support Pokémon boost JP by cheering during skipped battles?
When I was tracking JP values between battles, it seems that skipped battles use only your magikarp's JP and never included the support pokemon. Every battle I skipped had the same jump height at a given JP, there was no variation. If you are re-advancing through a league that a previous generation started and you get to a battle where the opponent has more JP than your magikarp, you will need to watch the battle instead of skip it in the hopes that a support pokemon will give you a boost to win. While I do not have hard data or documentation to back me up, I have checked the numbers several times across many different generations, JP amounts, and in different leagues with several support pokemon present in the training pond.
TLDR: Support pokemon do not help with skipped battles.