This condition affects my middle fingers to some degree, and I've taught violin students who show it much more strongly. I've heard it described as being "double-jointed," but that's not a terribly useful term, and tends to describe unusually flexible joints rather than this "popping and locking." (The image on the Wikipedia page, though, shows an extreme example of what you're describing and what I experience, an ability to flex the first joint (nearest to the tip) independently of the other joints of a finger.)
My (mild) version of this condition hasn't interfered with learning the violin, and I've been able to help several students around it. The key is to keep your finger arched as you press down. This is easier for violin than guitar, as our neck is narrower and finger position is more arched in general, but it can still help. In your video clip, your pinky is somewhat curved, and I find that in that "somewhat curved" position, the downward force intended to push the string down instead collapses or "locks" my second knuckle (i.e. second from the tip).
Instead, arch your finger just a bit more, so that more of your finger is "pointing to" the string rather than coming in at a "flatter" angle. Instead of pushing your whole finger generally "down," direct that downward force through the curve of your finger, the way medieval architecture used "flying buttresses" to direct the weight of a building:
Yes, you'll probably have to re-negotiate the position of your whole hand slightly to make this possible, and yes, it's harder on low strings than high, and might be harder for certain chords. But when possible, respond to this "locking" by arching your finger more.