Can creatures brought out by {birthing pod} be countered? Also, for phyrexian mana, can it be either or, or just whatever's highest?
Yes and no. Something like {voidslime} can because it counters abilities. A traditional {counterspell} type card cannot because the creature is being put into play by {birthing pod}'s ability and not actually cast as a spell.
Black Jester will correct me if I R wrong.
U R correct. {Birthing Pod} is putting creatures directly into play as part of the ability, so they are not being cast.
As for the second part of your question, Phyrexian mana is still part of the cost, it can just be paid in a different way. For example the converted mana cost (CMC) of {Birthing Pod} is four, (three colorless and one green Phyrexian). Good?