I say LEAVE IT IN. It may be that the metal wasn't as strong (thickness?) as the original but if it were mine and doing what you are doing, (that is replacement of the cowl) I would blend in the seam with body filler, primer and finish as with anything else. Stronger cannot be a problem, "Not as Concours" would more than likely be a deduction if noticed. OBVIOUSLY, the cowl has been replaced, that being said, it is already "not as delivered" and you are working (I assume) to blend in all of those welds and seams. I would NOT leave it "as is" though.