The problem with black powder is there are tons of "experts" on the internet.
FWIW- here's the actual skinny. Yes, you can substitute different "f" if done with some common sense. Just like smokeless, start low, work back up. In the North South Skirmish Association, many, many of us shoot 58cal muskets with 3f and that's completely against conventional thought. I shoot a 69 smoothbore with 3f. That said, we don't get stupid like many folks and think if some is good then lots more is best. When I hear of charges in the 90+ range, I wonder just how much of that powder is blowing out the muzzle and contributing nothing to the velocity other than to serve as some additional resistance to motion like the ball. My competition load for a 58 is 44g 3f and it will cut one ragged hole at 50yds, no need to burn more powder.
Now as for the ball not seated on the charge. Yes, you "can" ring a barrel but here's the conditions- ball seated about 12in or more from the powder, lots and lots of powder, ball not fully rammed because of fouling and that's an additional cause of pressure spikes. Often if the ball won't seat, the fouling is not in balance with the lube. That is a critical component to shooting minies well and in a round ball gun, it will keep you from ramming the next shot without using a hammer. If it don't fit, for heaven's sakes, don't force it, find out why it don't fit. To make this more clear, the ball won't go down because the bore is fouled. STOP and fix the problem and correct the load. Pull a trigger on that one and it is a pipe bomb of your own stupidity.
A little bit of space won't be any problem at all if the charge is a reasonable amount and the distance minor. Look at the chamber of a Sharps. Lots and lots of space in the breech block even if you fill the chamber to the end. No kabooms there. My Sharps is perfectly happy with a 40gr 3f charge and shoots almost single holes at 50. I measured the chamber capacity at 100gr, that leaves 60gr of "space" not counting the breech block. Then there are "patent breeches" in some muskets. That "stepped" chamber makes it entirely possible to use a small charge and not be able to seat a ball on it. Case in point- many of the "Zouave" repops. I have one with the patent breech and I can't seat a minie all the way down. If I just ram it till it hits that "lip" of the breech, it's all good. The gun shoots 2in at 50yd with 40gr 3f Swiss and that's with no serious load development and issue sights.
Upshot here- the seat the ball on the powder thing is there because there are lots of yahoos out there who will do something stupid. The substitution of grades of powder is possible IF you approach it with caution and reason. If the ball won't go all the way down, safely unload the gun and find out why.