Like Mark said, it's out of place on most longrifles. So if you are going for a historically correct look on an American-style longrifle, you might not need to worry about lining them up. When you look at old longrifles, the screws are (almost?) never lined up. (Note: You'll find an occasional screw lined up, but don't find the whole set of screws aligned. So that leaves you to wonder if even those the do line up were lined up intentionally. Of course, there may be exceptions...)
That said, if the build you are working on really calls for it, then you can use "gunmakers screws with extended heads" (Acer Saccharum's note above) to get them lined up the way you want. Or you can just make the screws yourself. The result is the same. To make this kind of screw, turn down (or file down) a rod to the size of screw you need, then thread it and fit it to the hole before you cut if off and finish making the head. Screw the threaded rod down snug in its proper hole, then mark on it where the slots should be oriented. Then pull it out, cut it off, file it to near finished shape, then saw the slot, then finish file it (or turn it, if you prefer).
When sawing the slots for that kind of build, you may want to grind the "set" off the teeth on a hacksaw blade. That way you get a fine, perfectly vertical slot without the rough edges left by the cross-cut set on the teeth.
But, again, if you are going for a historical look, it may not be necessary for your to approach the slots that way, either. It all depends on what you are trying to represent. The slots on some American rifles seem to have been filed by a very narrow triangular file, rather than sawed. So, all that is a reminder that it's helpful to study even those little fine details on any historical rifle that you hope to represent with a contemporary build.
Re your question about countersinks: "Also, how does one countersink so that the bevel is equal around the drilled hole?"
How many cutting edges are there on your countersink? In general, the more "teeth" it has, the less it chatters, and the smoother the cut. The smoother the cut, the easier it is to keep it smooth and even around the hole, and to get it matched up well to the screw head.