Normal? Perhaps if there is no other option.

I would get togather with the contractor and let him know you find his way
of running the pipe unacceptable and see if you can come to some agreement.
You may have to throw more money at him.

Keep in mind it is pretty hard for people sitting at a computer to give
advice on a given situation. It may be close to impossible to hide the pipes
any better. It may be what the contractoer was intending all a long!

The company I work for did the heating with a remodel in a multi-million
dollar home. The architect would no give us enough room in a wall to run
venting for a water heater and boiler located in a room below. We had zero
options, the venting had to go up inside the wall. I walked off the job
after talking to him about it. He was ****ed because "we" were holding up
the job. I told him he better call my boss an figure out what to do. The
wall went from 2x4 studs to 2x8 the next day.
Greg

Your points are all well made, and I will bring it up and see if they
can explain why they want to do it this way.

Do you think $3900 is a lot or a little for a 5 drop bathroom? The
entire room has been gutted to the studs and joists, so the upstairs
part should afford easy access.

Downstairs they have to deal with plaster walls and then a basement with
a somewhat confined crawlspace.

I ask with the understanding that I might not be providing enough
information.