I would be more concerned about here you lost 2 feet as that could be a huge problem

What if you we're to extend the upper vanity into a short "L" and tuck the toilet on the right side wall upper corner. Make sense?

Yes, where did the 2 feet get taken from?

The bonus room shrank by 2 ft. We emailed the builder on Friday addressing this issue and haven't heard back. In the mean time, I'm trying to see if there are better ways to reconfigure the bathroom with this added space.

If they haven't put up the drywall, they can move it to where it was in the plans. Unless you prefer it the new way.

(where is the bonus room? I'm thinking they are off on a couple of walls?)

You *could* have a double vanity on the long wall by the tub and then just put in a linen cabinet/wardrobe where you have the single shorter sink counter. That could give some visual separation for the toilet.

I'd be more concerned about your loss of 2 feet in the bonus room... unless that really was just "bonus" space that you didn't know what else to do with so it became a bonus room. But, if it was a planned area, you need to make sure you still have plenty of room for the furniture you planned and all walking routes through the room now that you are missing the 2 feet. This is the time to correct it.

I am still having a hard time grasping that the "only" change is the bathroom 2 ft bigger and the bonus room 2 ft smaller. Something else I believe must be incorrect and I would be very leery of going to far until you are 100% sure there will be no major issues going forward.