When the daughter of the Duke of Westminster married a Van Custem son, a bunch of the royals were invited including the Queen and Philip. Charles wanted Camilla to sit with him and the other royals. This is before they were married or engaged so it's against protocol. So Charles and Camilla skipped the wedding. I don't how much say Mrs Custem had in the seating arrangements. Since the bride's family is usually in control. The wedding was held in Chester Cathedral with the reception at the Duke's estate.
The protocol was correct especially with the Queen in attendance. Camilla didn't have any official ties to Charles at time. You saw the same thing at William and Kate's wedding. Chesly Davy wasn't sitting with Harry as his girlfriend with the royal family but Mike Tindall was since he was engaged to Zara.