I agree with picher although I'll push the range on an invasive animal if needed.
Picher, I feel like the difference in accuracy has to be the ammo, since my experience mirrors yours, in that 2 identical rifles (I have 2 examples of this myself) the 17 will outshoot the mag. Do you think it's the ammo quality or something else?
I got my .22 WMR to shoot some ammo at about 1.5 MOA at 100 yards, but it would still throw flyers more often than the .17 HMR.
Ammo quality seems to be a factor, though some brands don't shoot as well in my rifle as others. The CCI A17s seem to be the worst in my rifle. You made a good point on the invasive animals and if the distance is pretty uniform, or you use a rangefinder, it's easy to adjust for long shots. I'd probably do the same.