If you are painting the trim a different color than the walls then, yes, you would need to paint them separately.

Color Tile is often good, but some of the other guys will have super deals on their small lots remainders.

Removed old floor tile ( dark green ) from kitchen, dining and utility room and put in 18†neutral color Tile.

If this isn't possible, your best option may be to get a repair kit that allows you to mix up a custom color of putty at home.Filling Minor ScratchesFilling a few minor scratches on a laminate floor can be done with a wax pencil that matches the color of the floor.

Also recommendations on window colors too?

Black does not go with the color scheme.

They have 3 or 4 door styles/colors to choose from.  

Do you pick the colors?

No way would I let the GC get the items you listed except paint with you picking the colors.

They have painted the apartment professionally with great colors, installed a permanent stone fire pit in the backyard, maintained the deck and kept a clean yard.