Should I pay the underpayment penalty?

Dear experts, I filed extension this year, and my tax consultant sent the rest of the amount minus the Underpayment penalty of around $400 to IRS with my extension. Now when he is filing my taxes, this comes up in the amount owned in the State summary, but not in the efile. The underpayment penalty of $400 also showed up when I tried the same with TurboTax as well. He says it's ok and that I can pay it if IRS comes back. He told me that I can send the signed and scanned efile form to him and that I can pay that amount online if I really wanted to do that. Is it ok to not pay underpayment penalty? Would there be any penalty if I didn't pay that? Thanks in advance for your advice.