If I’m not wrong Ctrlr only stores the value of each modulator with the project (Atom, I would like to know this for sure, you stated several times that Ctrlr stores the current state of the panel, but this is not totally clear to me), so unless you assign the sysex dump values to different modulators the data will not be restored with the project.
Of course you can save to disk any incoming sysex dump, but later when you open the panel this data will have to be recalled manually (or maybe you can devise a clever way to load the sysex file on startup and send it to the synth).