In-universe, the transporter turning people into a muppet that can still see, hear, taste, smell and touch is basically transforming someone into an entirely new lifeform. There would be tons of implications in-universe. Just the Gorn egg thing for example. Gorn eggs can't be removed--but can the Gorn eggs even survive if a transporter turns the host into a muppet?
Do muppets age? Do they still have diseases that they had in their original forms? M'Benga's daughter might've had a perfectly feasible life as a muppet if that was the only way to halt her disease instead of literal non-existence in transporter stasis.
Like many other shocking technological developments in Trek (like transporters miraculously de-aging people in Rascals), this will be a one episode thing and never mentioned again.