So, with a 3.25" overall diameter at the breech I was thinking a 1" diameter powder chamber would be an adequit margin of safety.
I would buy that. But be sure the inside diameter of the tube is truly round so the breech plug fits tightly. A light shrink fit would be even better. You may have to bore the breech end to guarantee a truly round hole.
Should I be thinking about a truncated cone shape, a truncated cone with a hemispherical tip, or possibly a straight walled chamber with a hemispherical end?
Consider what you have the tooling and ability to make. Original Coehorns had a truncated cone with radiused corners which made swabbing more effective. Since you can make the breech plug without having to work at the bottom of a deep hole, there should be fewer limitations.
Also, should I chamfer the edge of the powder chamber or leave a square shoulder where it steps up to bore diameter?
Ideally it would be radiused to match the shot, but an appropriate chamfer can be almost as good.
Also, I assume a powder chamber should be just large enough to hold a standard powder charge.
Yes, although there is no established "standard charge" for golf ball artillery. You'll have to establish that yourself.
I might eventually make up a mold for lead or possibly brass balls, so I want my powder chamber to be as large as it needs to be to practically shoot these heavier balls as well.
Forget brass; too hard to melt and too expensive. ZA-3 zinc diecasting metal is about the best choice. Lead may be too heavy (about one pound for golf balls.)
Also, is underfilling the powder chamber a big problem?
That was the method used to adjust range with Coehorns as they had fixed elevation. If should not be a problem with golf balls, although it might approach a problem with heavy shot.