[zero the hero]

well what size is the enclosure? What tune are you trying to accomplish? Whats the difference in tuning between your "optimum" size and 5"?
In all likeliness the difference is miniscule and you won't notice. I'd use the flared.

 

[zero the hero]

Another option would be to use 2 inch flared ports as long as the air speed stays acceptable for your design.

But, a 2" port would have to be 1 1/2 inches long to equal the tuning of a 3" port 4 1/2 inches... that's called a hole

How about a 4" flared port?