Bath remodel: contractor set the closet flange 1 inch below the new tile floor and stacked two wax rings to make up the gap, and the flange centerline sits 13 inches from the new vanity.

Three code violations and a leak waiting to happen.

1. Flange Height (IPC 405.4 / UPC 402.6): The flange must be set on top of the finished floor. Setting it 1" low and stacking two wax rings is a "hack," not a method. Double wax rings are not listed or tested for that gap; they compress unevenly, creating a guaranteed leak path at the horn or the floor. The flange needs a spacer ring (e.g., Oatey Set-Rite) or a flange extender to bring it flush with the tile.
2. Clearance (IPC 405.3.1 / UPC 402.5 / IRC R307.1): 13" centerline to the vanity violates the 15" minimum required clearance from the center of the toilet to any sidewall, vanity, or obstruction. You have 2" less than code minimum. The toilet will hit the vanity, or the user hits the vanity. The flange must be moved.
3. Wax Seal Integrity (IPC 405.4): Code requires a "watertight joint." A 1" gap bridged by two rings cannot reliably maintain that seal under load or movement.

Fix: Demo the tile around the flange. Install a flange extender/spacer so the flange sits on top of the tile. If the rough-in allows, rotate/offset the flange to achieve ≥15" centerline to the vanity. If the drain location is fixed, the vanity must be narrowed or moved.

Bottom line: The contractor is wrong. This fails inspection and will leak. Require correction before tiling continues.

The contractor’s approach has multiple code and functional issues:

1. Flange Height: The toilet flange must be at or above the finished floor (IPC 405.3.1, UPC 405.3). Setting it 1 inch below the tile floor violates this. Even with two wax rings stacked, this creates an unreliable seal. Wax rings are designed to compress slightly (typically 1/4" to 1/2") when the toilet is seated—not to bridge a 1" gap. Stacking them risks uneven compression, shifting, or failure over time, leading to leaks and sewer gas intrusion.

1. Flange Support: A flange set below the finish floor lacks proper support. It should be anchored to the subfloor, not floating on tile or underlayment. Without solid backing, the flange can crack or shift when the toilet is bolted down.

1. Clearance: While 13 inches from the vanity centerline to the flange is acceptable (minimum 15" from center to any sidewall or obstruction is typical, but 13" may be tight depending on vanity depth—check local code), the flange height issue overrides this.

Correct Fix: Remove the tile around the flange, raise the flange to sit on top of the finished floor (using a flange extender if needed), and secure it to the subfloor. Then set the toilet with a single, properly sized wax ring (or wax-free seal). Stacking wax rings is not a recognized or reliable method—it’s a workaround that risks failure.

Tell the contractor: “This isn’t standard practice—it’s a defect. Fix it per code before I accept the work.” If they refuse, consult a licensed plumber. A leaking toilet can cause subfloor rot, mold, and costly repairs. Don’t compromise on the flange.