Which trucks will fit this Atlas car?

Someone has modified that. Originally it had a big plastic bayonet pin that went into the bolster. The threaded brass insert is an addition after the fact.

Put the screw you got in a drill, tighten it down carefully so you don’t crush the threads (or lock 2 nuts on the screw and load that into the drill chuck). Run the drill and file down the head diameter until it fits in the truck’s hole. I have done this before with good success.

If the hardware store is close by and well stocked. Bring the truck with you.  You could try an Allen Head. Often times the head is not much bigger than the threaded portion. The above mentioned method should work as far as making the screw head fit in the recess of the truck.
The only issue I see. There is no longer a mounting post for the truck. It’s pivoting on the screw itself. You may need to use some Loctite on the screw or just pop the shell and double nut it if possible. The screw has to be left slightly loose in order for the truck to pivot.

Nobody has modified that car, except for the brass insert in the bolster.  That was added so that 2-rail scale trucks could be installed.  The car is a white-box "old Atlas" car from the 1970's.  It came with plastic trucks and funky couplers.  The new Atlas trucks will make the car ride way too high.  Choices are:

1) Use Weaver trucks on the car.  They have a lower mounting point than the new Atlas trucks.  You'll need to take off the body shell and remove the brass insert (it should slide out when pressed from the bottom.  Replace the insert with a plastic rod or wooden dowel to plug the hole, then drill the rod or dowel to receive a small screw to hold the Weaver truck.

2) Remove the plug, cut down the thickness of the plastic bolster on the car, and use the Atlas truck you bought.  You'll still need to plug the hole and drill it for a screw.  The tiny screw that comes with the Atlas truck is no good, it is only used to mount the truck on a "new Atlas" car that has a different design.  I made a jig for cutting the bolster, but I'm not at home so I can't tell you the thickness of it.

Find a set of the 1970-era (of which your car is from) Atlas/Roco trucks with the original "two-rail" wheels, they really are of "three-rail" dimensions. I have a set that I can send you (email in profile); they will be complete with pin, wheelsets. and couplers.

Note the brake shoe detail:

I have been away from my computer for awhile. I appreciate all of the helpful responses. Next time I will know a little bit more.

The brass insert does not slide out easily and the plastic around it shows signs of stress. I don't want to increase the stress or break it.  While the car looks a bit high without modifying the bolster, I think I won't tackle that project right now. I am going to try @Boilermaker1 method and file down the head and then use two nuts.

Thanks