Typical pairings are constructed with
1) A two-way defenseman who produces points, plays tight gaps, recovers pucks, and makes a great first pass (#1 / #3 / #5)
2) A steady, sizey defenseman who kills penalties and generally boxes out the front of the net (#2 / #4 / #6)
Stone is a big defensive defenseman who kills penalties
and produces points. He's a #6 in terms of role, but he doesn't need a pure #5 to be successful because he's offensively capable. I value him as a ~3.25M player so 3.5 is an acceptable overpayment.
I guess he's a #5B or #5.5 defenseman rather than a #6 if you really want to analyze his role. He'll anchor the bottom pair but his partner needs to be a puck mover. He can't play with a guy like Clayton Stoner or Matt Bartkowski. But he isn't himself a guy like Clayton Stoner or Matt Bartkowski.
In many ways that's similar to Shea Weber, who's neither a true #1 nor a #2.