General Tile Discussion

I've been building a house near Carson City, NV for about 2.5 years (doing as much as possible myself. I'm getting close to doing the bathrooms and looking at the pebble tile my wife picked.

We have hard water and run a softener. Our current house is the same hard water and noticed the grout job was poor quality after watching hours of your videos. We get deposits on the grout line address of the tile and realized these are due to almost no grout and water sitting there and tons of mineral deposits.

Hence my concern about the new tile for the new shower floor. Looking at it, i noticed the pebbles are touching each other and would not allow grout between them to seal the way it should and afraid we'd have the same problem since it should allow water between the pieces.

The image shows 4 pieces together on the left with noticeable lines between the 4 sqaures. On the right side, (a little hard to see) i marked the packages with a sharpie next to each line where the stones touch each other. Looks to be at least 10% touch.

Any suggestions for this issue? I assume manually stack the whole floor, or try to pull out the ones that touch and fill out with a slightly smaller stone to leave a gap for grout?

I also suspect the only way to eliminate the lines between each square foot is to leave space and manually lay them a few inches between the 1 ft^2 tiles.

The shower is 5x6 curbless with glass walls around 2 sides.

I plan to use Prolite thinset on everything and Bostik TruColor grout. (any opinion on the TruColor?)