First about how to parse that English gloss: "indicates point of departure or separation of action" is a contraction for "indicates 'point of departure of an action' or 'point of separation of an action'" -- maybe that already makes it a bit clearer.
To dig a bit deeper here, it's no secret that many glosses in JMdict are by some sort of coincidence (lol) quite "similar" to the one's you'd find in 大辞林. So here's the equivalent one in Japanese: ⑤動作の出発点・分岐点を表す。 So basically this is supposed to be a translation of 動作の分岐点.
And as for what is meant by that: For example something like 電車を降りる or 日本を出る, where the action has a starting point inside of something but continues until the outside of it. That's a bit of a different concept from the meaning no. 3 (i.e. 参道を歩く where I'm walking on the shrine road the whole time and not leaving it) and also different from meaning no. 1, as the action is not applied directly onto that thing/location. For example by getting off a train I'm not doing anything towards the train at all, I'm just moving my own body.
I wonder what "separation of action" in the 5. means.
I wonder what "separation of action" in the 5. means.