Even if that were the case, shouldn't the letter state "You have a balance due to Virginia of $xxx. Payment must be made electronically at tax.virginia.gov"  The letter does not indicate a balance is due.

It was the case for a short period of time (2017 and 2018 tax years), when a waiver was required for a fiduciary to pay other than electronically, but that changed for tax year 2019. Here is a link to the VA tax website https://www.tax.virginia.gov/fiduciary-income-tax which states:

Return Payments

If paying after you file your return, you can make an electronic return payment using the 770-PMT eForm or Web Upload. 

If you prefer to pay by mail, complete the 770-PMT voucher and send it to us with your check or money order.