That's OK. If the car knows that the entirely mechanical opener was used, it can still drop the window a tad. My experience with other frameless doors is the issue of dropping the window a tad and raising are compatible with mechanical door releases (think anyone but Tesla)....
- You open the door (mechanically)
- Car senses that the door was opened
- Car slightly lowers window
- You close door
- Car raises window
You missed a step:
2.5 The damage to the seal is done.
If it doesn't have a sensor to intervene before the door is opened it may be to late. (Or if the response time isn't fast enough.)