its often more puzzling when you talk with the owners of the cars and listen to the list of stuff thats been done to the motor.
"its got 6-pac pistons, balanced, heads are blueprinted with a 3 angle valve job, balanced, rods resized with ARP bolts, (cam brand of your choice) with 22X @ .50....." etc, etc.

you hear the list of parts, and it seems like a straight forward enough build, and you wonder why its such a slug.
no one ever really thinks to themselves....."maybe the machine work is just crap".

for comparison, here are some numbers from a very clean OE 906 head.
this head is in excellent condition for a 100% stock head, and could actually be put back into service with just a light touch of the valve seats. doesnt need any guides or anything. this is as good of an example of an unmolested 906 as ive seen, although its not the best flowing stock 906 ive tested.

stock 906, OE valve job, OE valves, no back cut
lift----I/E
.100--59.6/48.4
.200-121.8/95.1
.300-182.5/125.7
.400-213.9/145.3
.450-219.6/149.1
.500-223.5/151.6
.550-228.5/152.9
.600-231.2/156.2

thats 30cfm better than the "16 second" head at .200 & .300, which is a big part of the flow area with a .450-.500 lift short duration cam.

i'm not saying its always the case when you see a particularly poor running OE type car that its the fault of the machine shop......but i have to believe that its at least a contributing factor in many cases.