There will be a bit of ambiguity in my answers...because there's no true right or wrong way. But here I go anyway:

1. Is the decision to go with epoxy or non-epoxy grout based primarily on resistance to mold and/or staining or is one type better than the other as far as preventing water penetration?

Epoxy grout will allow less water penetration than a cement-based grout. Being non-porous, it'll also be less liable to staining. I consider epoxy to be overkill in residential showers, unless you're into dying your hair in the shower, etc. One other thing, you have a kerdi shower. That will limit water penetration, so it's sort of one more reason that epoxy could be considered overkill.

2. If we don't go with an epoxy grout in the shower, would the Polyblend grout used on the floor be suitable or would you recommend something different?

Polyblend or any other manufacturer's cement based grouts would be fine. I use product from several manufacturers. Some people are preferential to just one manufacturer.

3. I think I'm confusing "caulk" and "silicone"... Are they used in the same applications? If not, what is the difference?

Think of silicon as a type of caulk. There are, in general, three types of caulk typically used in residential shower construction; latex, siliconized-latex, and silicon. Latex is easy to work with, but the least durable and the most prone to mold and mildew staining. Silicon is the most difficult to work with, but has the best water-repellent capabilities. Siliconized-latex is a hybrid, it's in between the other two.

In a well-built shower, any of the three could work fine, though I usually use caulks with some silicone in them, either S-L or 100% silicon. Look for a caulk that is color and texture matched to your grout, that way the caulk will look like your grout. Some 100% silicon's are only offered in color-match, but not texture.

Since you mentioned Polyblend, here's a link to Custom's Color Matched Caulk.

4. Is caulk and/or silicone necessary in a Kerdi shower? I have nightmares about mold forming on my caulk (or silicone?) and having to tear it all out.

The only proper way to avoid caulk completely is to do a floated mud shower with reinforced corners. Other than that, properly pitched surfaces, proper ventilation, and 100% silicon caulk will give you the best chance.

5. If we do caulk/silicone, I've heard that it should be done at every change of plane. Would this include areas that would not be taking a direct hit with water or having standing water on them?

Correct. In lightweight shower construction (tile backer board over wood framing, for example), adjacent surfaces can move independently of one another. Caulk will flex. Grout could crack. Now you have a Kerdi shower, that works in your favor, as water can only penetrate to the membrane. But in general, yes, for lightweight construction, caulk all changes in plane.

6. Specifically which product would you recommend?

A caulk that is color and possibly texture (sanded or unsanded) matched to your grout. A caulk that has some silicon in it. So the brand of caulk could be related to the brand of grout used if your goal is to color match.

7. Although our tile is porcelain, we are using a travertine base molding that has many nooks and crannies that will need to be filled. I understand that they get filled in by grout. This base molding is lighter that our wall and floor tiles and the matching grout that we're using there. Can I use a lighter grout for just the base moldings?

Yes, you can change grout colors within the wall itself.

8. Finally, would you recommend sealing everything once it is done? Or just sealing the travertine pieces?

I'd just seal the travertine. Porcelain is already non-porous. Sealing grout can be an adventure within itself. Regardless, use a penetrating, vapor-permeable sealer.

Thanks, Mongo, for all of the helpful info! That's just what I needed.

I am off-topic here, but treasuretheday - my shower will be very similar to yours! I love what you did with the bench and the tile. Do you mind telling me the dimensions of the shower & the bench (in particular?)

Our shower will be 68"x68" neo angle with 42" sides. We have vanities on both sides of the shower where you have it on only one side.

I am trying to properly size the bench and I love that yours has the clipped corners to mirror the shower!

What tile did you use and what granite?!

Thanks!

Thanks, Chays...

I just replied to your email but here are the dimensions in case anyone else is interested in building a seat with this shape...

The finished dimensions of our shower seat (as measured on the granite which has an approximate overhang of 1/2 - 3/4" inch) are:
Long sides: 20 3/4"
Short sides: 6 1/2"
Front: 19 1/2"
Height: 17 1/2"
Corner to center of front edge: 19"

The dimensions of the structure that was built would have been slightly different because of our 3/8" tile thickness and, of course, the overhang of the granite but hopefully that will give you an idea.

Your shower will be much bigger than ours! Our walls are (clockwise, if you're looking into the shower) 30", 50", 48", 8 1/2" and 24".

Our granite is Moxuara and the porcelain tile is Edimax Materia Forte in the Bronzea color.

We used 2mm (3/4") granite for the shower seat, curb and niche shelves, 12 x 18" tiles (with a 1/3 offset) for the walls and 4 x 4" tiles for the shower floor, ceiling and accent row.