Does this represent the true risk, in that your chance of dying in an encounter with the police is nearly 6 times greater if that police officer is male compared to female, or is there another explanation?
Female officers are vastly underrepresented in SWAT teams and other special teams designated to go after the very highest risk criminals (I am unable to find any actual numbers for this, but searching 'female SWAT officer' reveals a number of articles describing such an officer as the only female SWAT officer in her department).
Thus, the correlation is true, but the implied causation is backwards. If you are a barricaded suspect, have hostages, have an outstanding warrant for murder, etc. the officers sent to disarm you and bring you in will almost certainly be male. Given that you allowed things to escalate to that point without peacefully surrendering, the odds that when the officers make their move, that you'll represent a mortal threat and thus get shot is high.
The implied causation in your question is not addressed in the paper you linked, as it makes no attempt to account for victim behavior nor circumstances (at least as it relates to its discussion of the demographics of officers). However, there is an interesting tidbit that addresses a different point in your question:
Ridgeway compared shooting and non-shooting officers at the same scene (using data from 106 officer-involved shootings in New York City) and found that black officers...were more likely to shoot
Thus, despite white officers without normalization having a hazard ratio of 2 (per your question), black officers are more likely to shoot when on the same scene. Looking at Ridgeway we can see that they did look at the sex of the officer. While they found an odds ratio of 2.1, with a p-value of 0.29, it is very far from statistically significant. Given the low likelihood of a female officer at a shooting scene, it would almost certainly take a far larger sample than Ridgeway looked at to tease out the actual difference in risk.
Even Ridgeway has the confounding factor of victim behavior. Is there perhaps still a subconscious chivalrous behavior that reduces the likelihood of victims to have attempted to shoot at female officers vs their male colleagues?
Thus, all else being equal, are you six times more likely to be shot by a male officer than a female officer? Almost certainly not. Is there a somewhat higher risk? Very difficult to tell and I would be dubious of any study that claimed it had a definitive answer.