There really is no standard that we have seen in all our years of remodeling. Some contractor's say they do not mark up subs or materials but they charge a higher fee for the parts of work they do and for their services to make up the difference. In the end, one has to make a reasonable amount to cover overhead and hopefully some profit in order to continue in business. How they get to a price may be different, but the end price has to be competitive with similar companies and for same services. Where you will see big pricing differences is between a professional provider and 'Chuck in a truck'. The services provided are completely different.

This is always going to be an issue that is why when pricing a job you want at least 3 quotes and when I hire new contractors I make it clear that I will not pay overruns for things they should have been able to know when the job was priced so on my contract that is stated and signed off on and we review any overruns that could not have been foreseen so that we are all on the same page. I find this system works well for me and IMO I get much better quotes when it is understood from the beginning that they should know their business just as I have to know mine.