Thanks for this - answer from TA was that they use Amadeus. They make the bookings on our behalf and we don't have any access to their systems. The hotel booking does not appear in my ALL account, but the flight bookings on the same itinerary worked perfectly to appear as upcoming trips and no issues with airline status recognition etc.

Unfortunately our company policy changed recently and we can't self-book to expense it back anymore. I'd always do that previously to get rewards points on my credit card! Now our process has been "improved" to charge direct from the TA into our travel expenses account.