Electrical Bonding

Here's what i get from that, first the smaller than #6 thing....
The junction box needs to be bonded, tehy would like to see a #6, however, if a #6 is not doable, then you need your Minimum to be equal and no less than the wire size of the wires feeding the junction box (circuit conductors) from the panel, which would make it the bare ground in your 2 wire #12 feed wire.

With regards to the GFCI - it's the hairdryer in the bathtub scenario here.
Since your pump can't possibly fall in the pool from inside the garage, and most likely can't get a continuous wet and conductive path to the pool, it no longer needs to be on a GFCI.
The part that doesn't make sense to me is the behind the fence thing, it's still outside if behind a fence and threfore should have a GFCI protecting it since if it shorts during a rainstorm and you're barefoot, standing on the wet ground beside it, you've just become part of the circuit.

Either way, go with a GFCI, obviously another one of those MINIMUM requirements that's just better to go the above and beyond route.

As for the water bonding, I don't know about what the CEC says, but I tripped across it somewhere on the NEC yesterday and it ended up in my pile of printouts I took home to review with my electrician buddies.

If you're bonding your ladder, it's more than enough since it drops deeper than the low point on the skimmer at which point without the ladder your pool water would be "disconnected" from the equipment.

Another way to do this is to bond one of the lower screws on the skimmer. Even though the wall and skimmer screws sort of meet and touch, this connection can fail and is likely not considered to be enough, that's why the NEC want a sepaprate bonding to the water, doing so on the skimmer screw/nut would provide a good solid bond.

As for the beer, I'll take you up on it (and a swim in your lightning safe pool) should I venture to BC one day!