That is genuinely unusual, and worth understanding so you can recognize it when it is real versus when it is a setup for something else.
Most GC contracts are written one direction. The scope covers what was planned, and if the actual work runs over, the contractor brings a change order asking for more money. A change order is just a written amendment that adjusts the price or scope after the contract is signed. Very few contracts require the contractor to share savings if a line item runs short, so most GCs simply pocket the difference and say nothing.
What your contractor did reflects a particular billing structure, cost-plus with honest reconciliation. Cost-plus means you agreed to pay his actual costs plus a fixed fee or percentage for his work. If the plumbing rough-in took fewer hours and materials than he estimated, the honest version of that contract gives the savings back to you. Not every GC bills this way, and even among those who do, not all of them reconcile transparently at the end.
The thing worth knowing: $3,200 back on a $58,000 rehab is about 5.5 percent of the job. That is a meaningful number, and the fact that he initiated it rather than waiting for you to audit him tells you something real about how he operates.
In a market where capable crews are genuinely scarce (the strategy guide covers the current labor shortage in detail), a GC who manages your money honestly is worth protecting. That means paying promptly, giving him first call on your next deal, and not shopping his price the moment a cheaper bid shows up.
One thing I would confirm before assuming this is his standard practice: ask him directly how he handles change orders on future jobs, both over and under. His answer will tell you whether this was policy or a one-time gesture.
What does your contract with him actually say about scope changes and pricing adjustments?