Metamorphosis has a few peculiarities. Make sure one of the heroes is listed as a "dependency" to the other, and that they both have the same stats/resource costs (food, gold, lumber).
Other things like attack range, attack speed, movement speed, base health, base mana, base damage, damage dice, health regen, mana regen, and normal abilities (non-hero) can be different without problems on either form.
If you want specific abilities to appear on different forms, I recommend adding it but disabling it on map initialization for that player. Enable it when you need it. Though, this depends on what you mean by adding the ability too...
Also, god help you if you use a spellbook ability with Metamorphosis.
It can work, but it's a real pain to figure out.