For the 3 calibers you are loading, Unique is an excellent powder. If your batch of Unique is relatively new, I would suggest going to the Alliant web site and checking the recommended charges. The newer Unique has been changed somewhat from the old. It is supposed to be cleaner burning and somewhat less coarse so as to meter better. The burning rate is apparently a little faster than it used to be, as the current loading data shows some changes from the older. I don't think it would cause problems except for someone loading maximum loads.
Your thoughts on the case to powder ratio on these different calibers are totally understandable. The reason for this is the old original .38 and .44 cartridges were both black powder cartridges. Black powder is much bulkier than smokeless powder so the cases had to be large enough to hold enough powder. When smokeless powder began to be used the cases were actually too large. .45 Colt (aka .45 Long Colt) is the most extreme example of this. The .45 Colt cases are so large and the amount of smokeless powder needed is so small it can actually affect the velocity and accuracy of those rounds. With the advent of Cowboy Action shooting, in which very light loads are normally used, a new powder, IMR Trail Boss, has been developed. It is a very bulky powder that will pretty well fill up the case and still develop low velocities.
The 9mm Parabellum is a different story. It was developed specifically for smokeless powder and for a semi auto handgun. All semi autos, both handgun and rifle, need the shortest action possible for good functioning, so the smallest case possible was used. The downside to this is that the pressures are much higher. .38 Special pressures max out at around 16,000, the .44 Special at around 13,000, and the 9mm Parabellum at about 30,000. With 9mm pressures being this high, reloaders have less margin for error than with the over capacity revolver cartridges. Any variation in powder charges and bullet seating depth has a much greater effect on pressure than it does in the big over capacity cases. On the other hand, it is virtually impossible to double charge a 9mm, whereas it is easy (and has been done too many times) to double or triple charge .38 special, .44 special, and .45 Colt cases. This has resulted in blown up guns and in many cases injuries to the shooter.