the issue is I usually end up seating the ball much deeper than I had intended to and compressing the powder more than I would like.
Using a press will often compress the powder more too.
Maybe you could use some filler, cream of wheat, grits or semolina if you get a press.
Would you guess that your current paper cartridges are leaving any air space in the chambers or not?
Some folks make cylinder shaped "powder only" cartridges for consistency.
I'm not so sure about whether other cartridge shapes leave any air space or not, unless they're rammed and compressed enough to take the shape of the chambers and take up any extra space.
Since the .36 chambers are smaller than the .44, there probably wouldn't be as much potential leftover space as with a .44.
I don't think that leaving any chamber space is a safety issue, but it's only about being consistent.
However extra powder compression may be a good thing to do, especially with some substitute powders because it can increase velocity and perhaps consistency too.
A press makes it easier to compress or over-compress, which I don't know if there's even such a thing as to over-compress except maybe if using 777.
And even then, it's such a small charge that it shouldn't matter unless it shows up in chrony velocity testing or negatively affects accuracy.