I know of no module by Paulin that does the flange connection itself, only the nozzle-shell intersection.

With that said, I would speculate that the analyst before was placed in the position of qualifying something they themselves didn't really have much choice in, so resorted in cutting corners while reducing conservatism.

1e6 is a common go-to for bringing down CAESAR's 1e12 from the stratosphere down to the rafters, for a number of scenarios, such as normal restraint stiffness.

If the model features 1e6 on other restraints, it's possible it's an accidental mis-key from the restraint tab.

But I would ask myself, if, in the real world, we subjected this flanged connection to 1,000,000 lbs of force, would the flange move 1", or more, or 1,000,000 ft-lbs of force, would the flange move 1 degree or more, just looking at the flange, and not the piping attached to it?

I don't know the parameters of your flange, but I'd wager yes.

Is it typical? No.
Is it documented somewhere? Not that I've seen.
Is it non-conservative? Probably not.