It does affect the render, because Saber will draw any masks present. So when I’m viewing the first frame of the saber layer, I’ll see the correct mask(s) for the frame drawn, as well as like 4-5 other masks that seem to just “stick” there in place until their frame comes along (usually much much later in the video).
Separating the masks wouldn’t help, because I’d have to run saber on every layer, and it would still just “stick” until their frame comes along.