Hi Laura,
Applying a transformation to geometry is available for groups and components.
If your user rectangle is not a group or component, you'll have to retrieve what the user did exactly (translation, rotation) with its rectangle. That's not simple IMHO.
If at first you make a group with the rectangle, then let the user translate/rotate it, it's really easy to draw openings in the rectangle because you can retrieve the group transformation and then draw your openings at origin and then apply the transformation to them, or each time you calculate a point of an opening boundary, apply the transformation to it:
# Create the group;
group=Sketchup.active_model.entities.add_group()
# Draw the user rectangle here and let him translate/rotate it
...
# get the group transformation;
trans=group.transformation
# Apply the transformation to a point of an opening;
point.transform!(trans)
# Explode the group if neede at the end of the draw;
group.explode
Hope this helps,