Some variations on the output network.
Note that the supplies are already shown as bipolar, so I added a ground reference, implying the supplies are not just plus and minus of a single supply, but a dual, symmetrical supply.
Original
Two notes: 1. The transformer must carry the full low frequency content regardless. 2. LF transformers have high core losses at high frequencies. Might as well move the filter in front.
The supplies and phases are complementary and symmetrical, so we can divide the LPF in half against ground (or, since the ground terminal is just capacitors, it doesn't care what DC is -- either supply would work as well, if you prefer). This is identical if the phases are perfectly symmetric, so seems like a lot of component duplication, however in practice they will never perfectly match, and this provides equal common mode and differential mode filtering. Huge EMI win!
Continuing the symmetry theme, the primary can be CT-grounded without problems*.
*Given that the flux walking constraint now applies to both outputs individually, not just their difference. That is: DC output current must be very close to zero, for both outputs.
Also, as long as we're putting taps on things, the secondary can be tapped anywhere you like (not just half), getting the split phase that was asked about, or any other voltages for that matter.
Since it's symmetrical, we can even eliminate the transformer altogether -- assuming isolation is not required.
Now it is especially important for the LPFs to be independent, rather than balanced, because there's no potential filtering benefit from the transformer.
Tim