I was speaking to an S&B technician in Ottawa and he confirmed that the readers on Ottawa's buses run software from Metrolinx/Accenture, and report directly to them. This differs from Ottawa's fare gates and TVMs, which run S&B FareGo, and support internal cards like employee and accessibility cards, multi-day disposable contactless passes, and free transit for seniors on Wednesdays and Sundays with a Presto card, which isn't possible on the buses.
Apparently Ottawa is updating the BFTPs (bus fare transaction processor) to new software over the coming months to align them with the internal FareGo backend and allow them to support the various fare media that the gates support.