The plug is waterproof, preventing water from making its way from the door to the cabin. Once you drill holes in it you then have a path (the new wire) for the water to follow and an entrance for it to enter the vehicle (the hole you drilled).

A quick blob of silicon will prevent water from seeping through.

 

$0 couldn't prove one way or the other the cause of the BCM failure... no water has ever gotten into the thing though... i didn't make any new holes, i just widened the spot where there were no connectors in, in the big SMJ connector