"[The Congress shall have Power] To regulate Commerce with foreign Nations, and among the several States, and with the Indian Tribes." Article 1, also allows for them to make laws ensuring they can execute that directive.
Congress can, however, make laws whose explicit terms make their effect contingent on external facts, including the actions of officers in particular executive-branch agencies.
For reference. http://www.washingtonpost.com/wp-srv/national/longterm/supco...
“Regulatory agencies” are simply a label for a subset of executive agencies defined by certain traits; I think it would be very hard to argue that the Necessary and Proper Clause does not authorize creating agencies with these traits as a means of exercise of Congress other enumerated powers.
It would still be questionable that most regulation is actually within the enumerated powers. https://fee.org/articles/are-there-no-limits-to-federal-regu...
Saying there is no meaningful distinction is truly disingenuous. Like saying there is no difference between a fresh apple and a rotten apple. Obviously there is and there are reasons as to why the different states exist. One state is extremely beneficial and the other state is not.