Thanks.
So turns out this isn't possible just using the the 'with' attribute of the f:validateButton, even when the repeated entry is bound to a field (either the repeatER or the repeatED component).
I was eventually able to implement this using the f:invisibleEntry and some javascript functions (called on the onclick of my repeated checkboxes) to update the contents of the invisible fields. One can then use the 'with' attribute of f:validateButton to send the value of this hidden field.