3 is too many. Nix the limestone. It is high maintenance and will stain and etch much more than even the concrete.

Builders generally hire in house Design Pros for assistance. Why aren't you? Use your professional local contacts to find someone to assist you with your project.

The rule of thumb (for today's design tastes) is:

1 type of flooring though a SINGLE level with the exceptions being "kitchen and bath are allowed their own flooring choice".

Your comment about the master bedroom being "down stairs and connects to the living room" is confusing.

How many levels do you have in this home and where are the rooms situated (a copy of blue prints would be very helpful)?

If you have three different flooring types on a SINGLE level, you have too many floors.

K.I.S.S. rule is in effect (Keep It Simple Sam). Too much is too much. And you do know that stained/finished concrete is VERY SLIPPERY? Adding a slip resistant finish to the stained concrete in the master bath is going to increase your costs on that floor (and you need to have a professional concrete floor finisher on speed dial to make this work). As beautiful as stained concrete is, it can be hazardous in "wet" areas because of how slick they are. Special coatings are needed to reduce the slip-factor...and that adds costs. Just be aware.

As long as you have the right transitional pieces and design ideas in place this sounds like it will look beautiful. It sounds like you're going for an industrial look and something that can withstand the test of time. I like the direction you're going in. I would suggest the decor isn't too over the top but enough to tie each room together. Maybe similar artwork and furniture with area rugs? Just a thought....

"...stained/finished concrete is VERY SLIPPERY"

Polished concrete is within Tile Council of North America's standards for coefficient of friction, even wet.

The 3 types of flooring on one level can totally work, and can really enhance the atmosphere you are creating. One concern that did jump out, is the height difference and transition between the wood flooring and the stained concrete in the bathroom. Depending on your type of wood, and the substrate to be installed under it, your wood flooring could be as high as 1 1/4". As this is new construction, and if you haven't poured your slab yet, I would suggest recessing the slab in the bedroom so the wood thickness matches the thickness of your stone, then build up the bath floor to match the height of the wood. If this isn't possible, I would consider a tile that resembles stained concrete, or a tile that still gives you that concrete floor feel, that would give you some height to ease the bedroom to bath transition.