Yes, indeed Magnus, ColorFlow Pro can also create device links, in addition to device profiles and press curves.
I am not sure that a legacy Photoshop CMYK setup is the best option, if one is targeting GRACoL (at least the legacy Photoshop setup is flexible and user configurable when one has no other software).
Donateli, why do you have to re-separate in the first place? What is wrong with the CMYK input - is it not targeted at GRACoL when supplied to you? Is it something to do with the black generation? As you have found, there are trade-offs, whatever you gain by re-separating with the legacy Photoshop setting you are also having issues with primary solids, secondary solid overprints etc. It would not surprise me if you are getting very different output colour compared to the input from this conversion (independent of black generation, which in theory should not change the colour when done correctly).
You mention that you use the legacy Photoshop table to perform UCR... What don't you like about the input data, what benefits are you receiving when re-separating with the legacy Photoshop UCR setting saved as an ICC profile? Could you do the same or better with a different device profile than one generated by the legacy Photoshop settings?
Stephen Marsh