Yes, the alignment rod works to show moderator misalignment with the barrel bore, but not everyone has a rod sized just right for their barrel; nor one made of non-marring material. So, something we all have access to and is non-invasive may be almost as good: Masking tape applied over the muzzle face of the suppressor, slightly embossed with your finger to make a nice ring imprint. Then you shoot through the tape to see where the hole is relative to the ring embossed in the tape. A wadcutter helps, but is not essential. Usually, you can shoot a few shots without blowing off the tape to confirm system stability.
You can also look through the moderator after unscrewing from the other end after shooting through the tape one or more times - see image below.
Now, if you suspect large enough misalignment to cause clipping, then the rod is better because no shooting is required to get a reading. If you don't have a rod, you can look through the mounted moderator and barrel from the front end,
with the action open, and a light source at the breech. If your PCP has an easily removable bolt, then do that and look through the barrel from the breech. Else, the practice of inspecting a barrel from the muzzle with the action locked open, is standard for rifles such as the Garand and the M14; as scary as that may be. It is also how you tell that your lever action barrel is not obstructed, should you accidentally drop it muzzle down on soft soil while on a hunt. Better to look, than shoot out potential muzzle obstructions while hoping for the best.
Both the rod and the tape will show misalignment, but not the cause. That is for you to diagnose. Tightening the moderator on shims that clock it a quarter turn at a time will help you to identify if you are dealing with a problem in the moderator, or the airgun barrel stud, or adaptor. Is the offset rotationally phase locked to the moderator, or the airgun barrel, shroud, or adaptor?
Thanks to
@TorqueMaster for sharing this simple but effective technique with me. Here are two of his images of a custom extended shroud insert I designed. One, showing a pellet hole slightly off center in the masking tape; indicating the need for some diagnostics.