Imagine for a moment that the rain doesn't impact the final Group H match between Thailand and Indonesia. Football isn't played on paper but given how Malaysia beat Indonesia 3-0 and subsequently lost by the same margin to the Thai side, it would have been common sense to expect Thailand to beat Indonesia as well.
However, the weather played its part and just like the first match between Thailand and Mongolia, the conditions wrecked havoc on the plans of both teams.
Therefore Malaysia would have finished the group stage in exactly the same position, points, goals scored and goals conceded as Saudi Arabia, who were the sixth and final qualifer via the best runners-up route.
The teams would then have to be separated in terms of disciplinary points which Malaysia would have finished higher than Saudi Arabia by virtue of collecting only a single yellow card in the two matches against Indonesia and Thailand while the Saudis have six yellow cards spread out over two matches against Iraq and Bahrain.
So while the weather played into Malaysia's hands for a direct qualification as group winners, it wouldn't have mattered.