Unambiguous photon check is primarily used by the alignment, to get the best quality photons. The reconstruction for PID in Brunel/HLT2 does not use the information. Turning it off by default saves some CPU. Likewise, the beam pipe intersection check was primarily added to save CPU in the past, but now due to other developments costs more than it saves.
To see the changes w.r.t. !886 (merged)