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Is the fire place being used or will it be used?
Then you description is confusing/unclear. The pipe can't be in an active fire box but it's common practice to come up through the brick floor of a masonry fire place to feed a gas log. You mention a stove so that's what doesn't compute.
You can't bury a union connection to a flex. It has to be above the floor. It sounds like you have a gas cock that accessible in the same space so you're OK there.