I think what shortpants is asking is if the free-bore needs to be fitted to a particular length of bullet. I think you could ask a dozen custom rifle
builders and shooters and get at least a half dozen different answers. Myself, I like to be able to reach the lands with the bullet I am shooting, BUT that doesn't necessarily mean that I will seat the bullets to that length. I have found that seating bullets with a somewhat long jump to the lands doesn't detract from accuracy if the load has been developed around that much jump. There are just no concrete answers to questions about this.
Having said all of the above. I it were me shooting two extremely different length of bullets in one rifle I would set the free-bore so that the longest bullets would be seated fairly deep and work up a load with this COAL, and the shortest bullets seated as far out as would be safe and practical and develope the load for the amount of jump (if any) that is incurred with that COAL.