The height of the rod should be based on your height. That being said there are standard heights you probably want to keep. Those being 42" for short hanging x 2 ( x2 for double hanging) puts your top bar at approx 84" from the ground. The magic height of 42" is based on the longest item usually found in a closet - A man's suit jacket.

You obviously need to tailor the height of the rod to work for you, and your clothes You dont say how tall you are? And as for the height of the baseboard, its not really a concern.... It should interfere with anything. Not sure what your contractor has built for you, closet wise, but there are pull down closet rods you could get to make reaching the top bar easier.