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Would your charges really be any different than if that happened in a non 30.06 zone?
Yes. The self-defense statue (castle doctrine) specifically says deadly force is justified when:
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A person who has a right to be present at the location where the force is used, who has not provoked the person against whom the force is used, and who is not engaged in criminal activity at the time the force is used is not required to retreat before using force as described by this section.
If you walk past a 30.06 sign with a gun, you no longer have a right to be present at that location. You've violated 30.06 (trespass by a license holder). You will likely be arrested and go to jail even if it's a good shoot. Most self defense shootings don't end with the shooter going to jail. Most are investigated by LE, a recommendation is sent to the prosecutor's office, and then a grand jury decides whether to indict. If you're indicted, then you get arrested.
A property owner doesn't "press charges" for a 30.06 violation. Charges are brought by the state. It would be up to a prosecutor to decide whether to bring charges against you.
In your second scenario where the aggression begins outside, and an LTC violates a 30.06 seeking cover, etc, I don't see the state recommending charges. If you willfully violate 30.06 and have an armed confrontation, I could see there being issues.