They don’t do the same thing, and it doesn’t matter if two bonus actions have similar or even identical effects regardless. They are still two different bonus actions. They certainly don’t stack effects. The ability granting a bonus action tells you want it does, and that’s all it does unless...
There is nothing to wonder about or interpret. They are two separate bonus actions that do not interact in anyway, and you cannot use one bonus action to take two separate bonus actions.
Rapid Strike lets you use a bonus action to make one attack, and a reaction for one more. You can't use two-weapon fighting with it as written (unless you get a second bonus action somehow).
Setting aside you merely saying, "They can only use Sanguine Knot" with no qualifier for "before 10th level", it does what it does at level 1. Combat Directives is an upgrade of Combat Presence, not the core focus on the class. The pay off for giving you attacks is tactical versatility and the...
I just explained the argument for why that wouldn't work. The Invocation specifies both attacks are with the Pact Blade. It's about what effect gains trump through being the more "specific" rule in "specific vs general".
If Thirsting Blade is the more specific, it doesn't work. If Eldritch...
I suspect the argument would be that Thirsting Blade specifies attacking twice with your pact weapon, so using eldritch scythe would preclude the second attack. This is really a matter of which effect you think is more specific though.