Thank you for this analysis-
I think perhaps, you may have over-stated this problem.
I would suggest that as the DOD green building process gets more traction, more standards will appear and have commonality. COTS (commercial off the shelf) is a term seen more and more in contracting. This can mean, for example that DOD's "Green Certfied" can include products and methods already out there in the marketplace. No Recertification needed. (other than listing it as allowable)
As you know, the only time there is a deviation is MILSPEC if an item has to be designed & engineeed for a specific level of ruggedness, high tolerances, length of service, mean time between failure, etc.
Other cases where deviations occur would be if the contract is to be sole sourced, to be Set Aside, or as a preference for a HubZone/ or 8(a) contractor.
The sourcing examples above are what really take the time- not a COTS specification.
As simple contract codicil, Such as "COTS acceptable" would be fine, say - (If I may borrow your bikerack example)-
A bike rack manufacturer would be list that its "Super Bike Rack 2020! (made from forged recycled tank parts!)" is LEED cerfied (having been accepted by the USBGC people in a prior setting/use) Such a system could be like energy star. It's cerified /accepted already in th market- so it's a COTS item.
I would suggest, however, that you are on to something when it comes USGBC re-rating a building, if it hasn't been kept up LEED standards - (as in CFL's replaced with incandescents to save purchase dollars... becuase an agency didin't have the cash for CFL's, etc)
To continue- EBOM- Existing building and maintainance- That's the challenge. As budgets tighten, it's the operations areas where schisms between the DOD/DLA/GSA buyers and the USGBC certifyers will begin to appear.
Operating sustainably, in a consistent manner, in the coming budget environment, may soon seem quite pricey to the operations beancounters.