A builder should certainly not be moving windows without consulting you. That's a bad sign.

After spending over a year getting my plans to how I want them, I certainly would be miffed if the builder moved my windows or changed anything without first consulting me. In fact, my builder is on notice already that if anything needs an opinion or a change, he's to text, call or write me before making a decision. And he's gotten to know me well enough to tell me he wouldn't "dare make a change without consulting me first." LOL.

My builder texts us from the site if he wants to propose a simple change (move window set over 6 inches to center it on a wall) or calls us to the lot for a meeting if it's a big change (change a window's size because the architect didn't space the windows correctly). He does not make changes without our consent.

My experience is that plans are not perfect, and that field changes are almost always required. I'd expect the builder to consult and submit a change order if required.

The builder should certainly consult you with any proposed changes. It may be a good idea to make your expectations abundantly clear from the beginning. Respectfully, the homeowner should tell the builder how he/she would like proposed changes handled.

I'm hoping the OP is asking just to familiarize themselves with the entire process and not because of something that has happened. The builder should never change anything from the plan without consulting you first. If it's anything of significance, I would make sure the change request is documented in writing somewhere. I can't imagine any scenario in a custom built home where the finished product will be 100% identical to the plan though.