I am not entirely sure of what you're asking exactly, but I'll give it a shot.
Headspace of your chamber (in and of itself) doesn't really have much effect on your seating depth, because seating depth is generally measured from base of the case to the tip of the bullet or more accurately measured from the base to the ogive or bearing surface diameter on the bullet. The vast majority of modern quality rifles don't have many headspace issues IMO.
Now, there is a way that it could affect your seating depth. If your chamber has excessive headspace or saami maximum, and If you're using a modified dummy case or a case that's been seriously sized down to mimimun or less than mimimum headspace to arrive at your base to bearing surface measurement, then in effect; your base to bearing surface measurement will be shorter than it otherwise would be with a properly formed case that does fit and fill the chamber. Thereby creating more jump for the bullet if you were trying to use seriously undersized cases when shooting. In other words, we'd think the bullet is right against the lands but it isn't, instead it may be .020" off the lands.
The biggest problem I'm aware of caused by excessive headspace and/or FL sizing too much (oversizing the brass) is the possibility of eventually getting case head separation. After a few reloads of using this practice, you very well may pull the head off the case and leave the majority of said case in the chamber when extracting it.
I've only once had a rifle with excessive headspace that caused head separation, but modifying my resize process kept the rifle shooting just fine for many thousands of rounds thereafter, and I never saw the issue again.
One of the tools we can buy that will help in setting up our dies is the RCBS precision mic. It will also measure the headspace of a fired case and tell us if that measurement is in spec. They're available for most factory chamberings.
Aim small = Miss small