Guardian Skywatcher and Perfect Guard damage inconsistant

Firstly, as you may know, hitboxes in BotW are super tight.

Secondly, partial hitbox collision is a thing - the most common example of this is the "Bomb Impact Launch" (BIL). Depending on "how it hits", it can either cause minimal damage, and launch Link, or cause no damage, fail the launch, and Link gets hit by the explosion instead (ultimately causing more damage).

In the following clip, we can see that Link gets hit by the round bomb, knocking Link, but causing no damage, and then getting hit by the explosion instead. The rest of the successful BILs cause ~1 heart of damage.

Therefore, as you mentioned in the OP, the Guardian's swaying movements may have caused a "Partial Impact" on the hitbox of the guardian, causing less damage. Unfortunately, I have been unable to find more information as to the science of this at this time.