Ok, so I tried using the ESS Pin controls to Force Charge Pump to Off during Stop, but it makes no difference. I'm guessing that this affects the output only for the G-Code STOP button, and has nothing to do with eStop sadly. Seems strange that Mach3 could do this and Mach4 cannot as far as I can tell.
Taking Force9 at their word (that charge pump is redundant in ESS designs) I have switched the PMDX-126/107 to non charge pump mode instead, and the eStop now releases correctly.