Replacing plumbers putty with caulk/silicone between floor and bowl

We installed a Toto Drake on a somewhat uneven porcelain tile floor. There is plumbers putty between the toilet bowl and the floor which is about 3/8" in some areas. The putty has darkened, it attracts dirt, is difficult to clean and appears to be staining the tile (didn't know porcelain could stain). I would like to scrape the putty out to the degree possible and caulk (or silicone) over it. This is primarily a cosmetic issue as the putty looks awful. I realize I'll need to clean the base well to remove the oil from the putty so the caulk can stick. Does this sound like it will work? Any other suggestions? Thanks.

 

Do not use Silicone. See https://terrylove.com/forums/index.php?threads/polyseamseal-and-current-product-names.64887/

 

The bowl is definitely shimmed. I believe the putty was put in to fill the gap and maybe provide extra support. So do you think the putty can be scraped out and replaced with the Loctite product with the toilet being left in place, no resetting?

 

Yes.
Find the shims first so you don't disturb them.
Clean and caulk with the above mentioned caulk but in white maybe given the gaps.

 

I think that I'd consider picking up some foam caulk backer rod prior to caulking that gap. That would also limit the amount of caulk needed by giving a backing for the caulk rather than an open slot underneath the whole toilet. It needs to be slightly bigger in diameter than the gap to help prevent it from just floating around in the hole.

 

Thanks so much for the advice!