To me, one of the things I struggle with the most in this situation is a lack of information. Perhaps it's just the control freak engineer in me, but for whatever reason, I want to know everything I can about what's going on, and I just don't know a good place to find all the information I think I need.
One of the things I'm just starting to fully understand right now is the concept of the "pre-charge". If you already understand what the pre-charge is all about, or don't want to hear me mansplain it, feel free to click to another post. If you don't know, or want to check your knowledge against mine (and please correct me if I'm wrong about anything!), here's how I understand it.
The main battery has (of course) a very stable, high DC voltage on it. The exact voltage depends on the battery's state of charge, temperature, age, etc. To keep the battery from draining, and to keep things as safe as possible, the main contactor opens up whenever possible to keep the high voltage off of things that don't need to be powered at the moment -- in particular, the motor and its Sevcon driver. That makes things much safer to work on when the bike is keyed off. But those high-voltage circuits have a lot of "bypassing capacitance" (capacitors connected from positive to negative) to stabilize their working voltage, and they hold a charge for a fair while even after the contactor is opened up.
If the bypassing capacitors aren't at the same voltage as the battery, you can't just throw the contactor closed. The capacitors will want to charge virtually instantaneously from the batteries, drawing a REALLY high current spike just as the contactor is at its most vulnerable -- when the contacts aren't quite touching yet. That causes a fat, juicy spark to arc between the contacts, which heats them up so fast it can literally weld them together...and you don't want your contacts welded together. To prevent that, before closing the contactor, a high-power resistor is connected from the battery to the capacitors for a few seconds, charging the capacitors up to the same voltage as the battery with a much more manageable amount of current. The bike's circuitry verifies that the capacitors and battery are at exactly the same voltage before it will close the contactor, so there's no inrush when the contacts are closed, and no spark that can cause grief. That's the "pre-charge", and it's why it takes a couple of seconds before you hear the contactor click after you key on your bike or power up the charger. The SC adds even more capacitance, which it needs for its own operation, so the pre-charge isn't enough to reach full battery voltage, which is why (with the older firmware) you may need to key your bike two or three times before the contactor will close.
This, I'm pretty sure, is why an external charger can't just pull the contactor closed. The external charger can't do a pre-charge to the precise battery voltage because it doesn't KNOW the battery voltage before the contactor is closed, so it can't know when it's safe to close the contactor. That information has to be obtained from the bike's internal circuitry, which has access to the battery's voltage even when the contactor is open. It can verify the capacitors and battery are at the same voltage, and therefore it's safe to close the contactor. The onboard charger apparently also has that information, but I'm guessing the raw battery voltage just isn't exposed to an external charger through the Anderson connector, so it's never safe for the external charger to pull the contactor closed. Keying the bike on, or connecting its onboard charger, pulls the contactor closed safely, after which it's safe for the external charger to maintain the contactor in the closed position.
I think I understand it now (assuming I've figured this all out correctly), and it makes sense why you have to key the bike on to begin charging with an external charger. And it makes sense why not doing so can cause havoc. You're attempting to apply charging current to the battery without the battery being connected.