Why are you taking tax advice from a CFP ("Commissions Fatten Pockets")?  The 5498 is from the new trustee, right?  How is IRS supposed to know that it's the same money shown on the 1099R from the former trustee?  It could have been paid out in another year, or contributed more than 60 days after a check to the taxpayer was cashed.  

But the problem is created by the former trustee, which was probably the cheapest company that the CFP could find.  I had a client today whose IRA is with a major clearing house (Raymond James) that refuses to withhold state income tax.  My solution would be to move the account, but you don't get to be successful in that business without being a slick talker.