Sign a statutory declaration to say that you are happy to wave any warranty relating to the head work done by the dealer and you should be fine.
Dealers live on another planet to the real world at times however in this case I can see their point of view and would take the same stance, you are supplying them with a used head with no history, if a valve drops and the dealer worked on the car, the first thing you would do is point the finger at them, the dealer has not done the repair or supplied the head why should they take the risk?.
Itís hard for them to guarantee the work they have done if a problem/situation arises later on relating to the job.
If the dealer will not play ball then take it to an independent service tech if he is happy with the head work done let him do the job or let him supply a head that he is happy to fit to your motor. He would probably want to CC your head and that take a long time, head on head off a few time will cost you a few $$$$ on top.
He can then look after the car after that.
360ís only have 11.1:1 CR and is not supper high compression by a long shot, even if you skim 10 thou you will still have plenty P to V clearance, it will not detonate by lifting the comp up a few points, it may go to 11.6:1 itís still very safe CR on pump fuel.
The 360 motor was based on the R1 Yamaha head; a 1999 Yamaha R1 1000cc motor STD CR is 11.8:1 revving to 11,700 rpm making 150BHP, race guys would lift it to 12.5:1 with no problems.
I also have a good used 360 head if you need one. Why did you take a 360 to the dealer in the first place, were are you based?