Well, my guess, off hand is that, whether this is a carburetor or an articulated anvil, screws sitting at the bottom with empty threaded holes above, is a sure sign that they're supposed to be back in the holes. Truly, whether it's a clock, or a toilet seat.
And that any loose screw, still sitting in it's own hole, is supposed to be in that hole. Except that it's supposed to be tight.
Otherwise they're not doing their jobs. No company is going to spend money on screws that just sit at the bottom of an assembly, or uncontrollably loose in a hole. So they got there, presumably by not being put back correctly the last time it was apart.
I'm no Holley expert, but I would think that Holley probably has technical drawings and diagrams that should show (and even show in text) what those screws do, and whether or not they're supposed to be in their holes.
Looks to me like that is a "single-pumper" carb (vacuum secondaries I assume?) because instead of an intermediate jet plate (or whatever they're called) it's got a block-plate (or whatever it's called) that does not have secondary control circuits. So no jets, and no idle/air screws.
But you say it's a 650, which usually have mechanical secondaries, dual accelerator pumps, center hung floats, and all the usual suspects. Perhaps even a semi spread-bore base.
Got a picture of the whole thing? Or better yet, a part/model number stamped into the side somewhere? That picture has me very curious.
So yeah, put them back where it looks like they belong. Someone just left them loose or out when they put it back together.
Paul