I went with the lower quote in my last house to install a pedestal tub. It had a very slight leak and this guy eventually refunded my money and gave up trying to fix it. He said he thought it was because of slight movement when getting in/out of the tub was the cause. I ended up having it reinstalled by a very large plumbing company and it was 1K, they put some type of concrete like base under it to prevent any movement and they guaranteed the work.

If your builder is going to do the work for 1K and guarantee it I would go with it. Less hassle and no issues if any warranty issues later. At the most you would save a few hundred, however you could be giving up a warranty and it would just not be worth it.