No, there is no way to program hotkey to non-modal plugins windows because the hot key would only work it you first click on the window each time or possibly have the mouse over it. When you are working in Photoshop, Photoshop is listening for hot keys, not the plugin. When the plugin window is activate, it can then listen. However, since the typical workflow is you working in Photoshop, the Workflow Helper plugin would never be able to take control of the hot key events. This was discussed heavily in the Photoshop developer’s community after UXP was first released. As far as I know, Adobe hasn’t made changes to how it works.