I have chosen to live with mine by 'colouring in' the windowsills with a non permanent brown fine fibre tip pen (Staedtler lumocolor) - easy to wipe any mistakes with a moist finger. Incidentally I measured the sunshine window height of my original Mainline 3rds at 10.2 mm and to my surprise my early Bachmann Bk 3rd is also 10.2 mm, I thought Bachmann had modified the tooling along the Replica pattern where the windows are only 9.2 mm high! I remember the early Mainline models had a tendency to go banana shaped,and assumed the smallers windows made this less likely.
I would have a go at flush glazing if I could work out how to round the corners of an accurately cut acetate window panel.
Mike