You have thought the situation out very well. The cylinders must be larger than the barrel or lap bullets won't do their thing. If the 45's are all yours, I suggest that you open them all up to the same size so you can standardize your ammo. If throats are opened very much over standard jacketed diameter, it will hurt accuracy with jacketed, but most casters don't get cramps over that as they never shoot jacketed anyhow.
Point here is, if you do shoot jacketed and have a gun that is good with them, maybe you'd like to keep it just for jacketed. Time to keep it is before opening the throats!
My recommendation is to measure the barrels at the muzzle, then open cylinder throats at least .001 larger, then lap. Lap bullets produce almost no change in cylinder throat diameter, but only polish them a little, mainly because each throat only gets one while the barrel gets six.