A yes and no answer here. According to the electrical diagram in the service manual, charging through the booster post touches systems that are not closed off by the key switch in the off position. Because most circuits aren't complete when off they are protected. On the 2013 ST the accessory plug is switched, so that's out. By using the a direct connection to the battery the parts touched are the regulator, rectifier, and magneto/stator but are protected through the key switch because there's no completed circuit.
On the 2013 ST, at least Ann's, the break lights can still activate when the switch is off, so there are circuits that are on in the off position.
You're not wrong to charge according to the manual. I just recommend going strait to the battery as a belt and suspenders type of precaution. It's probably just my neurosis coming from the motorcycle community where you'll find they mostly go strait to the battery. It's also what my shop does for the Spyder.
Just my 2 cents.