First off not trying to be a dick about this BUT the old adage comes to mind in regards to your situation.
Would you bring your own steak to the keg for them to cook along with your own candles etc just to use their table and utensils? we all know the answer is NO so why should providing auto parts be any different.
I'm in the industry and see this day in and day out, yes sometimes parts are cheaper to buy yourself but your also not getting a professional red seal tech to install them and warranty that repair, its unfortunate they don't cover labour for warranty (We do where im a service manager) but hey everyone's shop is different. Its very expensive to run a business in the auto repair world or any business in general (wages, training, shop buildings, triple net, equipment etc) margins are in place for a reason to be profitable/sustainable or else whats the point? I cant speak on that shop but to me most of us all have our numbers inline with others, and diesel is a different world in itself and usually costs associated with those repairs sky rocket fast.
The auto repair parts world has turn this whole industry into a mockery, any joe blow can go down to the store and buy whatever part they want including parts that sometimes they don't even know what it does on the vehicle or where it goes! Causing major safety and reliability concerns for us in the industry.
NO OTHER INDUSTRY gets this issue that im aware of and please chime in if your in other trades aka electricians, plumbers, carpenters, welders etc. and do "Customer Supplied Parts or Materials"