Why gender the showers in the first place? Seems like added complication for little to no benefit by splitting into separate queues.
If you had them as self-contained shower rooms with changing area, that would probably be better from a personal standpoint and also alleviate the issue you raised.
Not the OP though, so who knows.
The restrooms have single line of stalls. There's a moveable wall between the stalls to change the allocation of how many men's stalls there are versus women's. That makes it so if you're running an event that tends to attract more people of one gender than the other, you can create more toilets for that gender. Quilting expo? More women's stalls. PC gaming event? More men's.