I have all my Cly and head work done by a local shop,Pearson Racing,he is a motorcycle machine shop only,hes been doing this for over twenty yrs,his rates are very fair,one of the guys i work with took his evo clys to a auto machine shop for boring and when he reassembled his motor it smoked,they had no idea that they were supposed to use torque plates,me personally i would rather take my stuff to someone in the motorcycle field,do yourself a favor and talk to several shops to get an idea of what you want,IMO i would steer clear of any shop that tries to SELL you on larger upgrades with their heads rather than working with what you have.
Not all Auto shops have the proper equipment,thats why you need to investigate and ask questions,to answer your question as to who did the work before MC shops,well the clys that were cast iron were a whole different ball game as today to each there own,all i know is that my 01 RG ,all the cly and head work was done by my local shop and that 95 inch motor stood up to 60,000 HARD miles and it never had one issue and i did all the assembly of the motor,its all about who you feel comfortable with.Some auto machine shops have been doing work on HD heads and cylinders for years and they have all the required torque plates and jigs to perform the work, you just have to check with the shop before having the work done there.
You would be surprised on how many MC repair shops use a local auto machine shop to do machine work on MC components.
Who did all the machine work on MC parts BEFORE there was MC machine shops??