Okay, with a self excited generator, the output of the generator will naturally follow a 'constant V/Hz' pattern.
A 12 pole machine means that if you apply 6Hz you would get 1 rotation per second, or 60 RPM. You could say that this means the output is 0.1 Hz per RPM. You have supplied the open circuit voltage of 0.5V/RPM, so that means that the output of the generator will track at 5V/Hz. I presume that this is the line-line voltage measurement.
Because the generator is operating in a roughly constant V/Hz fashion (ignoring voltage _drop_ due to loading), the transformer will not have problems with saturation caused by low frequency. As long as the voltage drops along with the frequency, the peak flux in the transformer core will remain constant.
If you leave the primary of the transformer unchanged, it should continue to function with this generator. If you reconnect the transformer in delta, then I suspect the core will saturate and you will see a bunch of problems. So I don't see you being able to get the voltage that you need by reconnecting the transformer secondary, unless you have a way of adding turns to the secondary.
IMHO the simplest approach is to use a different MPPT designed to operate with the higher voltage produced by your generator. However this might be an expensive or simply not easily available approach.
You asked about using a VFD as some sort of DC-DC converter. While I can imagine ways to 'hack' such a system together, IMHO it would be a bad approach. The power semiconductors of the VFD would be exactly what you would want in order to build a high voltage MPPT, but the control logic would be all wrong. Replacing the control logic would be a nightmare.
Given the hardware that you actually have, the first thing that I would look at is the winding connection in the generator. Perhaps the generator can be re-connected for lower voltage. In this case you might get the voltage low enough to use the MPPT you have, without the transformer.
The next thing that I would look at is the rectifier. If you can bring the neutral from the transformer, you could use a different rectifier arrangement and obtain a lower DC voltage. This might be a low enough voltage to use your existing MPPT, without the transformer.
The next thing that I would consider is using a different sort of rectifier arrangement on the output of your existing transformer. Take a look at 'voltage doubling rectifiers'. Through a relatively simple arrangement of capacitors and additional rectifier diodes, you can get a higher DC voltage than the normal output from a full bridge rectifier. As you describe your system, you simply need a higher output voltage to drive a 24V battery string rather than a 12V battery string. A voltage doubling rectifier might just do the trick.
-Jon