You are exactly right despite what builders will tell you. You aren't getting much for under $200 unless the builder is doing you a favor or is a friend charging you very little for his time,
On average expect to pay at least $75-100 in rod labor - This is pretty much going to be the money the builder will be making for doing your build.
Shipping the finished rod to you - This will vary to some extent depending upon shipping company, distance, length of rod, and insurance but expect to pay at least $20-25.
MSC parts and supplies for the builder - Epoxy, glue, and whatever other small parts or products needed - $10-20
Cost of materials to the builders - There are not many if any rod building product suppliers that will ship for free. Some will offer free shipping over a certain $ amount but will hit you with a $10 charge for an oversized shipment for the blank.
Just for the above items above you can easily be starting at $120 and you haven't even picked out a blank, guides, or any components. If you picked out a $50 blank, a $20 set of guides, and handle grips, thread wrap material, and a reel seat, plus any needed small parts like a but cap or winding check and you can be at $200 right there.
So IMO, you would need at least $200 to have builder do a custom rod for you without giving you a huge break on labor. If you want something that will be pretty nice and start to separate itself in terms of performance you really need to be around $250-300.