Plumbing – Toilet too close to wall

What it looks like is that you have a Ceramic Floor.

You need to use two flanges - the reason for this setup is that the pipe flange does not sit high enough for the toilet to properly seat against - the tile height is a problem its a bit too high. So the common procedure is to install a spacer or extender flange. Typically you will have a Caulking to Form a Gasket between the two lower flanges. Clink my link below to get the details.

Here is the options and a more detailed layout of what and why and how to resolve the issue.

How to remove a metal flange toilet gasket and replace it - some ideas for repair are included.

Since there is no flange installed yet you could just fill in the void with materials such as plywood or hardy backer to bring it up close to the level of The existing floor then solidly secure the new flange with long screws.

The wax ring mounting system of a toilet to a flange is fairly forgiving so you do not have to be precise. You could leave it the way it is and use a extra thick ring or you could fill it as I suggested and use a single thickness ring or one of the newer rubber gasket options. Having the flange above the level of the tile floor is not necessarily the right thing as this could be problematic in getting the toilet to sit tight to the tile floor without rocking . I would shoot for having the top of the flange be at the same level as the tile floor( or slightly lower ). You want enough gap for the wax ring or mounting system but not so high that it interferes with the toilet.

There is more than one way to skin a cat, there is no one correct answer for your question.

Many times when I lay a new bathroom tile floor I am able to unscrew the flange and lift it up and slide the new cement board underneath it but sometimes that is not possible and I have to use a thicker wax ring or a flange extender.

I saw a new product on this old house that was a thick squishy foam type ring that looks much nicer to use then wax.