Can I use Jegantha as a companion if I have an Apex creature in my deck because of the Alternate cost?
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.