Jonathan Davies and Regan King also added doubles for the hosts while Josh Turnbull, Rob McCusker and Sean Lamont crossed to beat their previous best of 53-11 against the Borders in 2007.
And Scarlets coach Nigel Davies believes Thomas could make a late surge into the national set-up ahead of summer Tests with South Africa and the tour to New Zealand.
Davies said: "Rhys has not had the greatest start to his Scarlets career and has had a lot of injuries. But he showed what he is capable of today.
"He's a very good ball player with the ball in hand. He has put himself in contention for Wales and done his chances no harm."