I might be wrong here, but even if the basic code behind the engines is the same (the sound generation part), M:C and ST seem to send different parameters in, as there are more/less/different options to change on both devices. And I tend to believe, that the Patches are stored as “Save the values of the macro-Knobs, the devices have” instead of "saving the core-parameters of the underlying synth-engine. Would be cool, if its different, but it would take up way more space to do so, instead of saving just a few macro-values.
On Top of that, they won’t sound the same, as everything behind the pure sound-generation is different (different Filter, different envelopes, different way how the sound is overdriven with the Volume+Dist knob).
I will get my Syntakt today, if nothing breaks the delivery car or its driver. We might be able to test that, if you would provide me (or anyone else with a Syntakt) one of your export-files.