I didn't read EVERY post above, but:
1) by RAW the beastmorph doesn't alter the class ability "mutagen" - it alters "swift alchemy" at 3rd lvl, "swift poisoning" at 6th, "poison resistance +2, +4, and +6, as well as poison immunity" at 2nd, 5th, 8th and 10th lvl, as well as finally "persistent mutagen" at 14th lvl. But it adds only effects on the mutagen class ability. This seems to be kind of bizarre/cranky (sry - my english isn't the very best, so i don't know, which word would be best to express my thought [looked to the dictionary])
2) you have to have the mutagen class ability to make use of those adds by RAW. That means, that archetypes, that DO alter the mutagen class ability to another class ability (I think especially of the mindchemist, who doesn't alter but replace the mutagen for the cognatogen by RAW), can take the beastmorph-archetype without use. They have to take the mutagen-discovery to get use of the beastmorph-adds.
Hope, I could get my point across to you and didn't repeat something already said above.
EDIT: to say, that beastmorph would add his abilities to his cognatogen, would be ok for me as a GM, but it's not RAW but RAI.