This sounds familar, but you have to get the PolyPhaser or whatever you use close to the earth. The idea is to establish as low resistance to ground as possible from the point of the device to the earth. And close, short, fat, heavy, and big means low resistance.
By the time you get your ground line from the PP to the earth ground when mounted up high like you suggest, your resistance may be well above that of the coax and then the PP will not have protected you as intended. In order to redirect current you must provide it an alternate path from a point close to the earth, a path of less resistance. The longer that path is the less effective it is and that is what I think you are suggesting by putting the PP up on the roof tower and then running a line down to ground rod(s).
All the coax (inside and out) must be protected as lightning current will be all over that coax. If I were you and had a roof mount I would keep that wire from the antenna mount going directly to a ground rod of its own. Just insulate it from the house. And I would also have the coax run thru the PP that was attached to another, maybe three ground rods spread out a bit down below the antenna just so the PP would have a good low resistance point to dump the current into. Put the PP right were you want it to work, redirecting the hit.