Manual VLAN pruning on a Cat 3550

I realize that VLANS 1,1002-1005,1006-4094 are prune ineligible with VTP pruning, but I'm wondering about the correct procedure for manually pruning these VLANs from trunks. Since you can manually specify what VLANS are allowed on a trunk, and since you can allow only the VLANS that contain ports on both ends of the trunk, here's the question.....Should you manually prune and observe the prune ineligible VLANS in the 'switchport trunk allowed vlan' statement, or is it OK to only specify the VLANS that are common to the endpoint switches? I'm asking this primarily as to what might be expected on the CCIE Lab exam.