The window height was determined by the workbench height underneath. As there is a 20-30 cm step down from the door, I think a 10-15 cm step up on the inside would feel really strange. Luckily it's not visible from the house, so we'll just leave it be and live with the weird lines.
Hang the door with the head height set to match the window, and have a small step over the sill?