I wasn't able to find a way to consolidate the changes in the plan

What do you mean by this? That the openings are only changed in the 3D view but nothing is changed in the plan?

In my case, it changes both the plan and the 3D view but the door/windows become distorted because their proportions don't match anymore.

If this is enough for your use case, you can have a look at the source code of the Pan3dView plugin

I need this change to be applied when rendering an image. I think that a new scene is built for the renderers and not using the same objects in the 3D view but I might be off here. If I am, then it might be enough to only modify the 3D view and leave the plan intact.