Sounds like you've done a lot of work on the floor, you might try spraying the walls with something like Lysol. Also, if your toilet stack isn't adequately vented, sewage smells will come in. You should see the stack vent on the roof, it will probably be a narrow pipe with a conical hat. If you don't see it, you're out of code and need a plumber.

I don't know whether this will work or not because you don't really know where the odor is coming from, but try an enzyme cleaner. Nature's Miracle is one, but there are others that some people think are better. Now, saturate the area around the toilet with it - and I am talking about soaking the area with this stuff. Get a gallon of it and pour some of it on the tiles. Spray it heavily on the vertical areas around the toilet. Let it dry and see if it makes a change.

I wonder whether the odor is from the wax ring that holds the toilet in place. Getting to that would involve removing the toilet and replacing the ring, so try the idea above first.

If you search Nature's Miracle on this forum, you will probably get the names of other enzyme products.

I think sometimes the urine runs down the toilet and under the rim on the floor where it's impossible to clean without lifting the toilet. Some plumbers will put a bead of caulk around the front part of the toilet to prevent it, but more do not. Apparently, you shouldn't caulk completely around a toilet because if a leak happens, the water can't escape and you'll never know there is a leak.

Graywings may be right about it getting into the wax ring.

I was a DJ in large nightclubs in the 70's and as you can imagine, this was a big problem with hundreds of party people using the restrooms every night. The floors were those small ceramic tiles with grout.

The only thing that ever worked permanently was a diluted solution of Muriatic Acid. I don't remember the ratio, but it was diluted with plain water, something like one part Muriatic Acid and several parts water. The Acid is nasty stuff so be sure you gloves and goggles. Hope this helps.

If you use something like vinegar or muriatic acid ( which is concentrated hydrochloric acid) you will cause the grout to break down.
I second the use of the enzymatic cleaner....it will remove the smell if you get it to where the smell is coming from.

Have you tried Clorox spray gel bleach? No need to dilute, just spray the heck out of it. It's not great for the tile grout, but it will sanitize and kill the smell.

Is the toilet wall mounted or floor mounted? My guess is that despite your efforts your can't really get under the mounting area. I'd suggest renting a canister type steam cleaner and using it around the mounting areas. The steam will force out built up grossness. It will probably take some time to get all of it out, but it will work. The other alternative is to remove the toilets and completely clean behind the mounting area. (not what I would recommend).

In our new build I caulked the toilets around the front and 2/3 of the sides to prevent urine from getting under the toilets. I left the back open to detect any leaks.

Did you try perixode? It works good with wooden floors.