Thank you for your thorough response! Actually that photo is the concrete subfloor, covered with Red Gard a waterproofing membrane. If I can fill the gaps around the flange with tiling adhesive that would be great I just wasn’t sure about the stability of that, as I don’t want the tile to crack once the weight of the toilet is applied and the adhesive perhaps isn’t quite level with the subfloor or it creates an unstable/unlevel surface. Also, I am nervous applying adhesive to the area that the toilet flange is bolted down into as it could muck up the bolts? Also to answer you question the toilet flange is bolted to the wood subfloor beneath the concrete subfloor and then the toilet will be bolted with screws that go upward into the toilet base.