I like the notion of disaggregating the control section
from the switch*magnetics section. There are PWM
controller ICs with digital outputs, there are digital
isolators and isolated FET drivers, the feedback only
needs to be itself isolated without bothering the
control loop stability / performance (current sense
would be tougher but believe I've seen that too,
in isolated forms). Managine or combining N current
sense feedbacks, that could be "interesting" (we did
this in ICs with multiple sense comparators in a
cellular "power farm", but at board level different
"stuff" might apply).
Depending on your end market sourcing appropriately
rated and qualified magnetics for 100A at all, let alone
fitting allotted volume and mass, might be your
biggest problem. A good argument for parallelism
I expect.