> whether this really all makes perfect sense to chemists themselves?

Yes. Obviously! Someone working in a technical field will understand the jargon and notation of that field.

Certainly if you are working in (say) physical chemistry, you might not be familiar with all the terminolgy of (say) organometallic chemistry, or vice versa.

The question of whether the audience might 'notice' is more tricky, but still bizarre. Certainly, changing (say) one part of a long chemical name might escape attention, but so what?

For example, one catalyst due to the prize winners is :

(5S)-2,2,3-trimethyl-5-phenylmethyl-4-imidazolidinone

if I swapped the '2,2,3-trimethyl' and the '5-phenylmethyl' parts of this, it would be likely non-standard nomenclature, and maybe someone might notice. However the information conveyed would be the same.