First, with --per-family-rates: you should find one file per family:
The second line should have 3 float numbers that should correspond to the DTL rates (I don't remember in which order, but it should be in the wiki). Do you obtain this file? If not, let me know, and you don't need to read the next line yet ;-)
If you have this file: apparently, if you run generax with --prune-species-tree (which is recommended to infer the species tree), we output 10^-7 for all three rates. I need to check if there is a good reason for this... Meanwhile, you can run generax using your inferred species tree and without the --prune-species-tree option to get some meaningful rates (same as your second run, but with --per-family-rates instead of --per-species-rates
Second, with --per-species-rates:
There is indeed a problem with GeneRax. By design, the per-species rates are computed after each SPR round. Since you are running with the RECONCILE option, we skip the SPR rounds and we do not compute them. But we should... I will try to fix this, but I won't be able to do it before next week. A possible bypass: You could try to run it with --strategy SPR and --max-spr-radius 1 (which should be faster than the default radius), but I am afraid this would also take a quite some time...