Unfortunately the experience you indicated is not the target but is becoming more commong with not MC shops, but many service, be it auto, apliance, etc.
Just poor ass poor service and professionalism.
I have been lucky with my dealer, for they do clean their mess from service and do so properly. In addition they seem to have the proper tools and will not do the classic crescent wrench and hammer for 90% of work with vise grips for the other 10%. They do seem to care about their quality and most of the technician have invested in the proper tools so that you do not get one using a close metric for the SAE.
Regardless of being lucky, I make it a habit of always checking over the bike when droping it off and more importantly doing a very close check of the area that were worked on and a general inspection of everything else. Best advice to all is to make sure that you do not get there at closing and then take the time to inspect while still at the shop with the tech, and any issue bring them up then. Also once things are looking good, if you get on the road and put in a few miles and something does not seem, feel or sound right, take it back immediatly and dicsuss your concerns.
Another tip, is that when you visit the shop, take a look around and see how their work spaces are. Are the benches clean, tools organized, rags stored, does it look like they have the proper shop equipment such as a real air compressor and not the home small Craftsmen unit. Is there organized libary and reference or do the SM manuals lay around all over the place with coffee stains, torn pages, is the computer piled under dirty uniforms or covered up with paint overspray. Are bikes that are being worked on or torn down having parts put away in labeld bins or bags, no mixing of one bike with others? Is there clean floors or are oil spots everywhere, spider webs in every corner like no one has done a shop cleaning in years, etc.
The shop condition and organization IMHO will give many a good idea of how they will deal with your investment.