Seu GM provavelmente está correto.

Se olharmos para as regras para Engula tudo, eles afirmam:

If a creature with this special attack begins its turn with an opponent grappled in its mouth (see Grab), it can attempt a new combat maneuver check (as though attempting to pin the opponent). If it succeeds, it swallows its prey, and the opponent takes bite damage. Unless otherwise noted, the opponent can be up to one size category Smaller than the swallowing creature. Being swallowed causes a creature to take damage each round. The amount and type of damage varies and is given in the creature’s statistics. A swallowed creature keeps the grappled condition, while the creature that did the swallowing does not. A swallowed creature can try to cut its way free with any light slashing or piercing weapon (the amount of cutting damage required to get free is equal to 1/10 the creature’s total hit points), or it can just try to escape the grapple. The Armor Class of the interior of a creature that swallows whole is normally 10 + 1/2 its natural armor bonus, with no modifiers for size or Dexterity. If a swallowed creature cuts its way out, the swallowing creature cannot use swallow whole again until the damage is healed. If the swallowed creature escapes the grapple, success puts it back in the attacker’s mouth, where it may be bitten or swallowed again.

Em nenhum lugar lá afirma que você é tratado como um item retido, portanto, não seria polimorfizado com ele. Da mesma forma, um familiar em uma Satchel Familiar não seria mesclado com você se você polimorfo, pois não é um objeto.

Agora, se olharmos para Polimorfo Maléfico, diz:

... If the spell succeeds, the subject must also make a Will save. If this second save fails, the creature loses its extraordinary, supernatural, and spell-like abilities, loses its ability to cast spells (if it had the ability), and gains the alignment, special abilities, and Intelligence, Wisdom, and Charisma scores of its new form in place of its own. ...

Assumindo que a criatura falhou no segundo salvamento, ela teria perdido a habilidade Engolir Inteiro, isso significa que você não poderá mais ser engolido por ela. Assim, você seria vomitado de seu corpo.