Your underlying premise is flawed, so none of your circuits are a good idea.
The simplest solution is to rectify all phases together to make a single DC supply. This mean one pair of diodes for each power feed line. It is unclear whether that will be 3 or 4 pair because it's not clear exactly what "neutral" is in your 3 phase system.
This resulting DC is going to be the input to a switching power supply that eventually produces current to charge the batteries. There is no reason to play games drawing power from only one phase at low torque. In fact that's a bad idea since it will increase the torque ripple. Instead, just modulate how much power you take from the raw DC supply. You can have the switching power supply stop drawing power altogether below some frequency, or otherwise draw power as a function of frequency. Of course you have to limit this to the maximum the battery can take too.
For a better quality but more complicated and costly scheme, you rectify each phase separately so that you can regulate the power factor each phase sees. However, you still try to draw about the same power from each phase. Separating the phases is only to allow for good PFC control per phase, not to allow for a different load from each phase. All the PFC front end supplies will dump power onto the same DC output, with a buck converter from there making the desired battery current. That buck converter takes into acount the frequency (rotation speed) as before. The loading the generator will see will be a function of how much power this buck converter is trying to draw from the DC voltage produced by the three PFC front ends.
The advantage of the PFC scheme is that, if balanced properly, will put a constant torque load on the generator. With the simple scheme, the generator will see some torque ripple at 6x the power frequency.