Also - you'll tie up a spot on the 40-man roster which otherwise wouldn't be necessary for his first 4 years. If your organization is reasonably deep with prospects, that means there's an extra one who will have to be exposed to the Rule 5 draft each year.
Still, if this kid's really in the superstud class and you're still not top bidder, you might as well make the ML offer. You've said it's "year end", so you're likely to be stuck with a pile of bonus bucks if you don't get him.