EStop should be seperate, with Mach only being notified that an estop has happened.
The charge pump should be used to either control drive enables, or via the BOB to deactivate outputs. Interlinking the two anymore is just a recipe for headaches later on.

(I will admit on my current retrofit project using a KFlop, things are a bit interlinked, but ultimately the physical e-stop circuit is not controlled in anyway by Mach. It's just that the KFlop monitors several other inputs for validity, and can trigger an e-stop within Mach if needed)