I’ve seen plenty of YouTube videos to know pretty much how to bed a rifle but my question is how do you cover the holes in the stock for the receiver screws? I have a particular rifle where the screw screws into the recoil lug. So how do I prevent The epoxy from getting into the female screw hole which is located in the bottom of the lug and into the screw hole which is located in the stock? None of the YouTube videos that I have seen show that explicitly

No idea, wax?  Vaseline?  Thinking it has a low melting point so it should be water proof but easy to get out.

Stick a drinking straw in the hole. Put release agent in the threads of the receiver and on the threads of the screw.

Use modeling clay to block off the action screw holes in the receiver.  The comment about the drinking straw for the screw holes in the stock is spot on - unless you're in Cali.

Put a layer of playdough over the hole and cover it and the action screw with release agent. That's what I did. Worked good for me.