Your carpenter did a good job given what you have. It looks fine and I'd hesitate to change it.

It took me a few replacement windows to figure out what I think works best but it takes ordering the window slightly differently The piece right beside the window lock - going out from the window is called a stile. It's on all four sides of your window.

Usually, the depth of the stile can be altered to fit the depth of the wall and then the final trim is attached flush to the wall and with a slight reveal of the stile. Again, the window itself has to be ordered with an extended stile.

When you need to match existing window trim, even with an extended stile, there is no way to do the sill correctly... The best "patch" we've found is gray bondo.

What we did find is that the manufacturer's stiles can be removed (pella) completely. Then, we just did the normal build out for the sides and top and used "regular" sill that was cut like all the rest of the sills in our house. No extra "layers" or reveals or weird patches.

We had to remove the pieces before the windows were installed. I think this only works well when you are completely rebuilding a window opening.

Now I'm frustrated. None of these windows were replacement windows. Our remodel took a garage and made it into a powder room, part of the kitchen, laundry room, etc. Plus we added a large room to the side of the house. I'm going to end up with these sills for every new window.

So you're telling me that it wasn't necessary? That, especially where we built an entire new room, the window stiles could have been ordered for the depth of the walls?

And for the new windows that went into existing walls, there was an option to remove the manufacturer's stiles and add correct depth ones?

Seems like this issue should have come up earlier?

Actually bmore, I think it is called a jamb extension by Marvin, but I agree that this is the issue.

Marvin Windows appear to come with a 4-9/16" standard jamb (to fit in standard wall thickness), and extended jambs need to be ordered for thicker walls. Your walls appear to be thicker than usual framed construction.

I would see if he could make a sill that would fit over that eased edge on the bottom and make a flat sill but other than that I would not do anything else.

For what it's worth, some casement windows are designed with sills that are distinctly bi-level, depending upon the hardware.

Nope. The stile is the vertical frame members of the sash. The part you are referring to is the extension jambs and stool [or sill] Most window companies make a stool for their window for a given wall thickness, but I think that installation and trim job look fine.
Flat? yes, in a perfect world. Windows are made differently these days. What does the display window look like where you selected them?