Rule 1 says "VTCA 2012/13 Rules, except as varied hereunder, shall apply" and Rule 3 says "If the team batting first is dismissed in fewer than 20 overs, the team batting second shall be entitled to bat for 20 overs" which matches the one-day rules. The idea of a one-day game stopping once a result had been achieved was tossed out due to bonus points. This suggests that bonus points are indeed being applied.
There's also nothing in the rules as to how many teams progress from the round-robin to the knock-out stages. I think it's the top 2 in each pool, but there's nothing to say that is the case.