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One possibility is to use a transformer.  The power input can then come from across the plus and minus input power.  The output can be referenced to whatever you like, which in this case would be ground.  The output current would always return to ground, so not effect the current balance between the plus and minus input supplies.  Here is the basic topology for a flyback converter:

<img src="https://electrical.codidact.com/uploads/39chBuNVQpfJrGDdWypR9LqE">

It does seem a bit clunky to use a transformer when isolation isn't really needed, but it does completely solve the problem of input supply imbalance.  The switching topology is also simplified because you don't need buck-boost.  Overall, maybe it's not so bad.