Due to their somewhat unique role, this may or may not be acceptable to Duty Holders further up the food chain
If I may I'll move away from the specific of the shackle bolt to the more general ethos and apparent "sharp pencilling" which may have gone on in RAFAT.
For most of my regular career and still quite a bit now as a reservist, I've been involved in the writing of regulations, both flying and otherwise. In the military context, they are always - at one level or another - "our" regulations.
If they are inappropriate for a specialist unit, then change 'em. I'm not competent to judge whether RAFAT needs the CT that a 100 Sqn shag needs, but IF (a very big IF) RAFAT needs less, or can (sensibly and safely) double count sim slots, then it's hardly rocket science for the Regs to say: "Except RAFAT, see Annex X for their requirements."
I always used to say that Regulations shouldn't be broken - not from a dictatorial standpoint, but from the (to me) common sense one that if the Regs are unfit for purpose - then get them changed (with appropriate staff justification).
If they ARE fit for purpose - then bl%%dy well comply.