I recently left a similar comment on another SE site. I posted an answer, it was accepted, and then the next day, somebody else posted a better answer. Because I think my answer is still useful, I don't think it should be deleted. However, the OP has moved on and will probably never change the accepted answer, so I commented to that effect on the (in my opinion) better answer.
For people who are inexperienced in the field (or just new to the site), that giant green check mark is like a flag saying "This is THE canonical answer." They may not be able to compare two answers and determine which is better just by looking at them. Voting helps, but once an answer has been accepted, no matter how many upvotes the other answers get, the accepted answer will always be at the top of the list. If the author of the accepted answer concedes that another answer is better than theirs, it is a strong indication to me that I can take that big green check mark with a grain of salt.
Obviously, this is not always the situation, but I don't think blanket-flagging all "this is the best answer" comments is a good idea.