That's exactly what I do. It will line itself up with the groove, no problem. The shaft of the tool is completely supported by the rod groove, so it has to scrape its way downward (or upward, since the stock is upside down...). It centers itself in the hole as it goes further in.
I'm scared to death of thin wood under the ramrod (or anywhere), so I'd rather have the hole go up than down. It ends up almost the same as a straight hole would be on the top, but with more wood left on the bottom....more or less. With the smaller hole, you have a little more room for variance. My holes always drop down just a little bit towards the bottom of the stock when I drill them, so even though I may start out at the 3/8" level, by the time it reaches the end, it has dropped down just a little bit, so it works out. Don't ask me why, but it does. After 15 years, I finally think I have a handle on drilling ramrod holes.
Did any of that make sense???