Should prep be inside the square-foot install rate?
Only if the rate states what prep it includes. A rate that silently includes “whatever we find” cannot be compared with a rate for installation on a ready substrate.
Under the finish
Flooring bids pick up unexpected money in the substrate. The honest estimate either describes the prep that was measured or excludes prep that nobody has seen. A blanket “5% patching” is a guess dressed up as a quantity.
Slab-on-grade, a topping, wood joists, a gyp-concrete pour, and an existing finish left in place are different starting points. The demo of the existing finish is its own area.
Labeled as an allowance because no survey was assumed.
Area times an assumed depth is only as good as the depth. If no survey exists, exclude leveling or carry an allowance the bid labels as an allowance, with the depth written next to it. Do not convert that allowance into a firm quantity.
A flat slab can still be too damp for the adhesive, and a dry slab can still be too uneven for large tile. Keep the moisture scope and the flatness scope on separate lines. The moisture page on this site explains the test methods.
Related reading: repair examples, moisture tests, tile on an unready floor.
Only if the rate states what prep it includes. A rate that silently includes “whatever we find” cannot be compared with a rate for installation on a ready substrate.
Patching follows the condition, not the room area. Columns matter when you are measuring the floor finish. They do not create a patch quantity by themselves.