I'm building a mutate deck and since the deck meets the conditions for Jegantha, the Wellspring I wanted to use it, but since I'm running a few of the Apex creatures and their mutate costs don't meet the requirement I wanted to know if Jegantha also looks at alternate costs or if it only looks at base cost for the requirement.
The mutate costs don't matter; you can still use Jegantha as your Companion. Jegantha states:
No card in your starting deck has more than one of the same mana symbol in its mana cost.
Mana cost is defined in the rules:
202.1. A card’s mana cost is indicated by mana symbols near the top of the card.
Costs of other abilities that may appear on a card, including mutate costs, are not the mana cost of the card itself, and that is all Jegantha is looking at.