There are a number of words that I would consider better, clearer when used in different situations.
"Clock" or "clocking" is perhaps most used in the UK when referring to dial and dial test indicators. This is probably due to the physical resemblance between the dial face of these indicators and the face of an analog clock. This seems to be a long standing usage and is probably considered proper in the UK and other places that were influenced by their usage.
From that I get the impression that many types of alignment are referred to as "clocking" because those dial and dial test indicators (aka, clocks) are used in the alignment process. But this most frequently refers to a linear positioning: it's use for an angular one seems to be less common and probably related to an angular process that uses a DI, DTI, or some kind of circular device with a rotating pointer.
I am a US engineer and I like using terms that are more precise and less likely to lead to misunderstandings. I have not either heard nor used the terms "clock" or "clocking" for angular alignment of any type. This is just not the best, clearest terms for any of these tasks. The terms that I would prefer would vary by the angular task that is at hand. So, if I were setting an apparatus to a desired angle, perhaps using a protractor style scale, with or without a Vernier, I would probably use the word "set" or "set the angle". Someone mentioned the alignment of two or more images. To my mind, image alignment is a linear task, not an angular one even when those images are being created with rotating drums. For such a task the work "alignment" seems to be more descriptive. And if you get into the rotation of the drums that are creating those images, then the word "synchronize" seems to be a better way to express what is needed.
When spark plug timing is needed, the word "timing" is what I have seen commonly used and it is probably the best one for that situation.
"Clocking" could be used in any or all of the above situations, but IMHO, it is not the best word to use. I suspect it is used in an attempt to appear to be "cool" and that is not a good or sound engineering practice (again, IMHO).