I prefer the flooring to go under the toilet.

If you need an operating toilet, the toilet can be set for use during construction. Then simply pull it for the flooring installation, then reset.

I'd want the flange height of the toilet properly set for both floorings; the thicker tile and the thinner marmoleum.

Part of the issue is sanitary, in that you have a cleaner installation (literally and figuratively) with the toilet set on top of the finish flooring.

I much prefer having a sanitary surface (tile, or whatever the finish flooring might be) under the toilet instead of the toilet having bare subfloor or underlayment underneath it.

The other part is "future-proofing". If you ever change out the toilet for one with a different footprint, the flooring will be where it needs to be.

Thank you Mongoct. I am using a contractor but the project has grown tentacles, somehow, and I'm trying to create mini-projects within the contract. I'm fearing that all "finish plumbing trim-out" will fall to the last days, a time at which the contractor will have almost all his money and I won't have a single working toilet. It's too scary for me. I'm breaking the project up. Thanks for your advice.

I'm going to try to get him to finish the bathrooms before the kitchen cabs are delivered. I don't have a sense as to whether it costs him more to get a plumber out sporadically than to have him for a solid run of days, but I can't trust. If it costs more so be it. I started with a house that had bathrooms, and I've put in a lot of money, and I now have a house where you can't make a pit stop. Too nervewracking for this poster.