It seems pretty clear to me that the intent in Girl Power, in listing 13 deaths before Roberts, is to include that one supposedly final death at the start of the TVM. That would have been the death of his 13th and final incarnation (in the sense of distinct regeneration), but that life was revived and prolonged, and then found a new body in Bruce.
This means, according to Missy, the Master died three times after inhabiting Bruce and before becoming (well, being brought back by the Time Lords as) the War Master. But this one source does not trump all, and she's only going off memory and giving a short account, anyway. The Eighth Doctor failing to mention certain companions before his regeneration (in TNOTD and the TDOTD novelisation) does not mean that other sources featuring different companions no longer truly happened. And Missy gives a completely different number in The Bekdel Test, as noted.