The answer is right there in the document (and, by the way, also
here).
"All applied parts (B, BF & CF) and grounded (e.g. enclosure class I) and non-grounded accessible conductive parts or
non-conductive accessible parts (enclosure class II) are grouped together and
connected to the ground via the 1kΩ measuring device (body model)."
In practice, you may have a problem deciding upon a "non-conductive accessible part" on Class II equipment, but your test instrument (Fluke or whatever)
will be connected to PE (as the diagram shows). But the diagram clearly shows a test lead connected to the enclosure, so it's up to you to do that (however futile that may seem in terms of Ohm's Law).*
Frankly, I would not worry about that particular test too much ... after all, what magnitude of current readings are you expecting anyway? If the Class II equipment is electrically unsafe, that will become apparent in other tests ... especially if you can find a
conductive accessible part on the enclosure (as required by the insulation tests).
Here is a tip:- if you really want to understand EST, you need to look closely at the various circuits. They actually tell you all you need to know ... and the Rigel guides illustrate them most clearly. Didn't the course you took spell that out? But don't worry, there aren't that many, and they should be easy enough to learn.
* I think this is where the "foil" technique comes into play. I have seen folk use an old ESU return plate and sit the Class II kit on that (at least that way the flying lead has something solid to clip on to). Opinions on the efficacy of that idea seem to vary, and you may find life becomes easier if you simply adopt whatever your mates do in that regard.