First of all... engine sleave is a wear item... over long time the bore will turn from perfect circle into oval shape. This is because the way crankshaft and combustion forces on the connecting rod... tilting it one way or the other. This is primary reason of losing compression.
By pressing old sleeving out and put a new one in, you are bringing it back to factory new spec. Perfect circle and thickness of the sleeve. By overboring it, you create thinner sleeve and weaker... which will not be stable for high compression diesel engine... thus engine will break down sooner... much sooner as this diesel engine runs very hot. There is always appreciable wear on diesel engine unless your compression is still high... but unlikely.
The valve, the machine shop is also correct. Because of continuous opening and closing, the valve seat wears out ir cokes thus also creating poor seal. So even if you put in a new valve, the seat does not match the new valves and will wear out new valve faster.
Let the machine shop do both for you and the engine will be just like new. They will measure the heck out of everything and make sure they are within factory specs. As far as the camshaft, I'd suggest you let them measure them for you also... you will need new valve lifters to match new cams. If you do plan to reuse old cam and lifters, make sure you mark them accordingly... each one is worn and seated to certain direction and if put in different lobe... will wear out that lobe faster than normal.