zog is going to want to shoot me, but here it goes:
There is NO restriction that says you SHALL NOT work on equipment above 40 cal/cm. It is a Fine Print Note recommendation in NFPA 70E - 130.7(A). It is a recommendation, not a requirement.
That being said, I would recommend adopting the recommendation. You should keep your 100 cal suit, however, because you will still need it for actions such as voltage testing, etc.
Now, to continue the discussion:
"If there was a breaker connected after the trasnformer secondary but before the secondary switchgear bus (not direcly coupled) then this would constitue a secondary main breaker and therefore protect the bus."
Yes, but remember now you have just moved the hazard from the whole bus to the main breaker. The high energy level is still there between the main breaker and the transformer output, and it should be lower on the LV bus section (provided correct coordination exists). You will still need to adopt another method (which Zog's paper discusses) to totally eliminate the hazard if you wish to operate the main breaker. The other method, of operating the Xfmr high side disconnect to de-energize the bus may not be possible if this is not a load break switch, without first opening all of the load breakers.