“So if the chilazon was some other creature and the murex trunculus was around and could dye the same color as techeiles (which we know it could because it’s the same color as plant indigo) then according to the kesef mishna the murex trunculus would be nichlal in kala ilan.”
the kesef mishna never meant that everything is called kla ilan, rather everything that color is nichlal in DINIM the gemara says for kal ilan. for example on a talis shekulo techeiles kla ilan can’t be used as chutei lavan so too anything else that color. and anyway the gemara in menachos is muchach that kla ilan is a specific thing.
about the ben yehoyada that says based on arizal there is ??”? on anything not real techeiles the sefer hakanah is mevuar that the mekor of the ??”? on kla ilan is talui on the fact it grows from the ground.