A few years ago the subject of holes in the gas locker with bolts through came up. Rob of the BSS stated, in writing, that if the bolts were properly sealed then that was acceptable. Not sure if i can find where it was posted on here, but I have it printed out.
As for going through the side of the boat then I can't see that that is a problem, after all there is already a big hole there. The thing is to stop the chance of gas getting into the inside of the boat, including the engine space.
OK, it was posted on 6th January 2013:
"Bolting a mounting plate or restraint anchors into the locker is ok provided the holes are fully 'filled-in' with no visible gaps/holes. These should also be quasi-permanent arrangements, not say access or inspection plates designed to be regularly bolted and unbolted."