Say I want to buy a car, a good car. I go looking and first place shows me a car for $45,000 and says it is great and a top seller in the country. Second place shows me one that is $100,000 and says its the best on the market. Third place shows me one that is $250,000 and says there is nothing else like it on the road. Which one is best, they are all good cars? If I ask for a detailed breakdown is that going to help? If I stated up front I was looking for a budget 4 door sedan with good gas mileage, good reliability, and not flashy its pretty clear which one is the right one.
When I give bids it can go a few ways. IF the customer brings me a detailed scope of work I will give them a price for their detailed scope of work and if the other contractors had that same detailed scope of work the quotes are apples to apples. If someone comes to me with an "idea" and wants a price I am going to price it the way I do it and the only guarantee I will give is that I won't be the cheapest bid you get. We will even do open book pricing, similar I guess to a cost plus situation, we state upfront what our rates are and what our profit will be on top and we will show you the books where every hour is accounted for, every receipt is shown, and a line at the bottom showing what our profit is. What I won't do is give you a break down of every line item because that is a ton of work and likely will change later on and then the customer complains about the change, or I have to eat it cause they won't pay the difference.
If you want a line item quote you are gonna pay me for it and there will also be a contingency line. If I am giving you a quote and assuming all the risk you better believe I am going to make it work out in MY best interest and not yours but I am going to make sure you get the job you are paying for because my reputation rides on that. Why shouldn't a contractor make $250k?
Also, typically, when bids are written with allowances, that isn't a set number. I do that fairly often too, with things that are unknown, which happens to be excavation and concrete quite often. I will put in a $30,000 allowance. If the work ends up at $20,000, that's what I charge. If issues show up partway through and I can see $30,000 isn't going to be enough, I have a conversation with the customer and let them decide how to move forward.
I'm not sure why people get bent over what business owners make. There is a lot of risk in owning a business, if a business is taking advantage of poeple and screwing them the market tends to correct that situation real quick.
It sounds like your handshake contract was a little wishy-washy and that is really where the problem is but still it sounds like you got what you paid for and at the end of the day what does it matter what the contractor's mark up is? It's really irrelevant to the situation.