There have been several posts about this family here on Rootschat - I see some not replied to, but this one was.
https://www.rootschat.com/forum/index.php?topic=854540.9Glancing through them quickly, I don't think anybody had found the parents of John with wife Marie de Mott.
Added:
There is a tree on MyHeritage which gives the father of Thomas as Jacob Bevan Rouffignac, born at Puyeasquier, Gers, Midi-Pyrenees. No date given or any indication where that information came from. (according to Google maps, that's 340 kms away, so possibly a little unlikely!)