Conference
 

In Federation softball: When the catcher goes out to talk to the pitcher, can a runner on first base go talk to the 3rd base coach without it being an offense charged conference?

No restriction on the offense talking to coach if the defense has called time and vice versa. NCAA is the only rule set I am aware of that requires offensive players to stay on base during a time out by the defense.

As long as they are ready to go at the end of the defensive conference there is no penalty.
At least in USA rules.

So, we agree that this is no problem and not a conference.

With R1 on third and R2 on second, F1 pitches a ball to B3. F2 asks for time to talk to F1, which is granted by the umpire. As she walks toward the circle, the runners leave their bases to confer with the third base coach.

Not a problem in USA Softball, NFHS, and virtually every other softball organization that I'm aware of with the exception of NCAA. In NCAA play, runners may not leave the vicinity of their bases to talk to a coach or each other when there's a players-only defensive time out.