If a disaster happens, like floods, then a decsiin has to be made on the spot. There is no way regulations can be written to cover everything. Just spectacular rain would be no reason to stop, neither would slippery roads, or possibly even mild floods (plenty of that in Toir of Britian a while back, the race ploughed on no problems).
When a finishing circuit is used, if it's less than a certain size, the time for GC in a stage race is taken at the entrance to the circuit first time. This helps cover the possibility of stopping groups if it's smallish and lapping or mixing of groups might happen. It helps a clean finish for spectators and stage results.
As has been noted, with the shambles on stage 1 of TdF, decsions to change finish point then, changing back again, a crash in the last 6km would mean everyone in the peloton at the time gets same time. This was because the move of finish was 3km to go, so the 3km rule was applied at 6km to go, then kept like that because of all the confusion. Not anywhere in the regs, but a good decision was made.
It would have been interesting to see what would have happened had there been a massive crash including all the sprinters and GC riders with 8km to go. Cue frantic chasing because there would be no same times given that far out.
As a rider you are often unaware of all this going on (no radios except at world tour races), which can be a good thing. Ignorance can at times, truly be bliss!