Hi Jenney,
Quick answer:
Unfortunately, this isn’t an uncommon problem. Stone tile in a shower is susceptible to this issue, especially on the floor and the bottom row of wall tiles. More so with showers built with a surface waterproofer (vs. traditionally built showers with porous mud bases that have waterproofing under the mud pan and behind the wall substrate).
Moisture issues:
The moisture can get in through the face of the tile, through the grout and into the edges of the tile, or through the grout and into the bottom of the tile. That means that changing your caulk by the drain or at the perimeter won’t do anything to improve your situation. By the way, while you can get epoxy grout, epoxy caulk isn’t a thing. The whole reason you have caulk is to have a material that flexes/deforms between two different materials or at a change of planes (like wall-to-floor, or wall-to-wall) where slight differential movement between the two won’t cause an unsightly crack.
General thoughts on sealer:
Sealer is probably the most misunderstood product when it comes to tile. Sealer is meant to clog the pores of tile enough so that if you spill a potentially staining liquid on the tile, you’ve bought yourself a few minutes to clean it off before it gets past the sealer to cause a permanent stain. Sealer is not meant to keep moisture out because it’s not capable of doing so to a high degree. You may then say, well…why not use it? What can it hurt? Won’t it do some good? While most modern sealers are breathable and will allow moisture to evaporate that’s gets into the tile or grout, they tend to slow down the process enough where it causes more harm than good. You think it’s taking a long time to dry this unsealed shower out now? Wait until you seal it and moisture gets trapped again…it’s going to take even longer to dry.
Contradictions in applications:
Depending on the tile, the application, and the sealer itself, the “rules” of sealing can also seem contradictory. For instance, there is a such thing as 6-sided sealing of tile to try preventing this moisture-darkening problem, but you need to be highly aware of incompatibility issues that make the thinset mortar not stick. And it’s not guaranteed to work…it might make the moisture problem worse by slowing down the evaporation of moisture that gets in. And it’s nearly impossible to do on tiny mosaic tiles without them falling off the mesh netting. And it’s a moot point for you, as your shower is already built.
Different types of sealer…generally, there are two:
1) an impregnating sealer that, once cured, leaves the stone indistinguishable from an unsealed stone….and
2) an enhancing sealer which generally darkens the natural stone to the color it changes to when you wet it with water. This enhancing sealer would mask your problem by darkening all of the tiles. However, I can’t see how matte or polished your tiles are. A polished marble face doesn’t usually like to absorb sealer. I wouldn’t use any sealer on almost any shower, but if you try this…please do a test before committing to the whole thing because you cannot realistically reverse the process.
Onto the next topic:
A surface waterproofing membrane under natural stone tile in a shower may contribute to more tile-darkening issues like you have than a traditionally built shower that has a porous “mud” base, but…
…natural stone tile in a shower is a gamble. There are plenty of pros that absolutely will not install natural stone in any shower, irrespective of what method of waterproofing is used, because of the very problem you’re having. No matter how pretty the tile looks in the tile showroom and no matter how much the salesperson claims that they “have never heard of a problem like this”, a certain percentage of pros will not engage in installing it. The problem you’re having is not predictable…sometimes it’s a problem and sometimes it’s not.
