Very few reloaders really understand rifle chambers and what goes on inside them. For openers, the body of the chamber looks just like the case that goes in it. The shoulder of the case is the stop. The distance from the shoulder to the head is where the headspace measurement is taken. On belted or rimmed cases, the case headspaces on the rim or belt and the shoulder should not limit depth. The throat of the chamber is where it gets confusing. The throat is cut to accommodate the neck of the case and comes to an abrupt stop. Beyond this abrupt stop is a slightly tapered rifled bore. This tapered rifled bore transitions into the true bore. This transition area is called "free bore", even though you would think it is "free" of rifling, it really does have the tapered beginnings of lands & grooves.
When a bullet is seated to SAAMI spec, you can see there is quite a bit of space between the ogive and the actual bore. This allows the bullet to move forward quite a bit before it contacts the rifling. Seating the bullet out to .010" from where it touches the rifling is optimum. The further the bullet has to move, the more velocity it picks up, thus more bullet damage. Combine the cant with the forward movement and you are certain to get bullet damage. If the bullet touches the bore, the chamber pressure will increase considerably.
Lets use a 308 Winchester for an example. The SAAMI minimum spec for the throat measures .3034" long. The diameter for the throat is .3435". The free bore should start where the throat ends and extend .020 to .100, depending on the individual gun. You'll notice the throat diameter is about .0355" larger than bullet diameter (.308) to accommodate the thickness of the brass case and a little room to prevent seizure. Manufacturers have learned that a chamber cut to SAAMI minimum specs won't work with all ammo so they cut the throat deeper, make the diameter larger, and extend the free bore. Here's where the accuracy problems come in.
I measured my Win Mod 70, 308 Bolt gun. It shoots sub-MOA groups as long as I do some tricks to compensate for the chamber. The throat measures .333" long (about .030" deeper than spec). The throat diameter is .348 (about .004 larger than spec). My free bore measures .040".
So what we have here is a throat that is bored too deep and ends up with an over sized space that should be the transition area (free bore). This condition is commonly but incorrectly called "excessive free bore". It really is too deep of a throat. If I trimmed my cases to the SAAMI spec in the reloading manual (2.015"), I would have a space in front of the case mouth that is .030 too long and a diameter that is .040 too large. This loose area gives the bullet an opportunity to move laterally or cant slightly on its way to the bore. When a bullet strikes the bore with 50,000 lbs of pressure and is ever so slightly off center, it will damage the bullet on the side that first makes contact. Now you have a bullet that is slightly out of round (oval). When that bullet goes down range, spinning very fast, it will wobble a bit and cause the point of impact to vary from round to round (loose groups).
If you were able to use cases that were .005 short of the free bore, accuracy would improve however, chamber pressure would increase. Now if you seat your bullet out farther, accuracy would improve even more and chamber pressure would go down. By doing both techniques, chamber pressure will be about the same as a case loaded to SAAMI specs. Usually, we can't get brass long enough to fill the deep throat so we end up with just the bullet out farther. I've found this requires a little more powder to achieve the same velocity and best accuracy.
There are some other things that will reduce bullet damage thus improve accuracy. The case mouth needs to squared so it will release the bullet straight, just like a barrel crown. If the case mouth is slightly off or if there are splits or irregularities, the bullet base will be forced off center causing the tip to enter the bore off center. Bench rest shooters like to turn the case necks to make the brass a very uniform thickness. This helps a great deal by getting the bullet started straight. Annealing brass is another trick that really helps. The brass is very soft so it will release the bullet much straighter than work hardened brass. I anneal my brass instead of turning necks and find it works quite well. The brass needs to be annealed every 2 shots to maintain desired softness. Annealing also helps compensate for a loading press or a chamber that isnt perfectly straight.
I didn't mean to write a book here but looking back at your post, I never did answer your question.
The case neck is much larger in diameter than the bullet (by .040" in the case above) and don't occupy the same space. Having the case longer does not change the overall length of the loaded round nor does it interfere with bullet seating depth, it just occupies undesirable empty space.
When working up loads, start with your bullet seated out to .010 from the lands. Then adjust your powder for the best load. By doing it your way, you would be changing the internal case capacity each time you change bullet seating depth, thus changing chamber pressure and velocity. You're chasing your tail. What you want to do is first minimize bullet damage, then adjust for best accuracy by changing the powder charge. Many reloaders get this sequence wrong and waste time and materials looking for the magic combination. There is one problem with extending your bullets; the cartridges might not fit in your magazine. If not, you can single load or you can seat to the max length that your magazine will accept, then work up your powder charge. This won't come out quite as good but may be a necessary compromise.
When you trim your cases, even the ones that are shorter than spec should get their mouths squared. A squared mouth is more important than a few thousandths in length. Usually you only have to do this once for the life of the case.
Sorry for the post length but I hope this helps you understand chambers a little better.