The question about signal propagate in trace or cable

My bigger concern here is signal integrity and managing that - I'll revisit this at the end. Ignoring that for now...

Case 1: This won't cause timing issues. If the propagation times for both clock and data are the same then there will be something there for you to use at the receiving end - even if the delay does amount to multiple clock cycles.

Case 2: Again, assuming no external timing influences then the receiving end of the MGT link can recover both clock and data successfully.

Back to signal integrity - you mention 'voltage distribution in the trace or cable'. You also mention 'hundred metres' & 'hundred miles' - both pretty tough challenges. If these distances are to be covered for either case 1 or 2 you are going to need additional buffering/boost circuitry. I would immediately be looking for an off the shelf solution (like a Gb Ethernet Phy) to do all the hard bit for me.

This option aside; whatever external circuitry you add is going to introduce jitter, which will reduce you're ability to recover the data at the receiver. In the case of data & clock you will also end up with a skew between them, which will likely be different board to board - i.e. non-characterisable, therefore not a workable as a solution. The compromise will be a trade off between data rate and distance.

Cheers,

Alex