I fear to even comment about the "great Crossrail toilet debate" but suffice to say this issue is raised every single time that the Crossrail senior management sit down in front of the London Assembly Transport Cttee. There is usually an annual slot for them to update the Cttee on progress.
Every time the Crossrail people (usually T Morgan and A Wolstenholme) politely try not to roll their eyes and say the Sponsors (DfT and TfL) did not specify on board toilets. However the Crossrail people have repeatedly said that all of the new build stations will have public toilet facilities.
I believe it is also the case that a reasonable number, but not all, existing FGW / TfL Rail stations also have toilets available. Given the full staffing promise that TfL make for their rail operations then I expect that toilets will be kept open during the hours that Crossrail trains run. Clearly we are 2 and a bit years away from seeing if that promise is kept about station toilets but I expect all hell will break loose if, for some reason, it is not kept.
And much as I might like to comment further I won't for fear of being shot down in the never ending crossfire.