I would guess that when AF wrote the historicals, which was after she'd named the present-day family, she deliberately named the historical characters after the present-day ones. She had already used Geoffrey, Lawrence (twice), Peter and Nicholas/Nicola as modern Marlows so it made sense to use the same names for the ancestors. By then she'd used Giles for Mrs M's brother so she didn't need a historical Giles. Karen Rowan and Virginia wouldn't have fitted into the Elizabethan family - but she could have used Ann.