Not exactly sure I'm following...there is an adjustment of the linkage for the pump. Is this the question?
I interpret the instructions as:
Metering rod arm should just barely touch the pump lifter link when the pump shaft is bottomed out. Mine touches well before the pump bottoms out.
To correct this condition, do I adjust at the external pump linkage? Or internally at the little arm where one would adjust the metering arm?
I was interpreting your post as “don’t worrry about adjusting at the external linkage.” But I have have misunderstood.