Theoretically, the recoording of the pass should trigger a reimbursement, at whatever rate is agreed between the operator and the LTA. If the pass is not recorded, then no reimbursement is made. Since, in London, all revenue stays with TfL, then the operator couldn't care less!!
Again, in London, the scheme is administered by The London Councils (LC), a grouping of the London Boroughs that acts on behalf of the Boroughs in many ways, and in London receives ENCTS funding from the DfT (as does every LTA outside London). So in theory, the acceptance of the pass should trigger a reimbursement from the LC side to TfL. It therefore follows that TfL, in being unable to record an ENCTS pass, is not receiving income, and the LC are not paying TfL.
However, as the number of ENCTS passes from outside London being used for travel is miniscule in the grand scheme of things, and the current TfL machines were configured for Oyster, and not ITSO, it has been let drift. I daresay that the new TfL machines will be both ITSO and Oyster compliant.
And before the usual suspects bang on about incompatibility, the TfL machines are 2003-ish technology . . . Ticketer is 2015-ish technology. Life is awfully different now, isn't it !!
You did ask . . .