Having learned the art of bedding fittings from some of the masters at Hinckley Yachts I believe in the bevel/chamfer and tighten once method for most things. I don't generally subscribe to the "tighten over a few days to create a gasket" method.
Beveling the edges of the holes does a few things:
1)It forces bedding compounds into the hole, like a funnel, as you tighten the fitting.
2) It creates an o-ring of sealant that is about 6-8 times the thickness of what would be there without a bevel.
3) It allows you to tighten the fitting all the way down without coming back days later to do so which can break the seal that has already cured around the bolts threads.
4) It creates a surface area that forces sealant against and around the bolts threads or shank.
5) It prevents gelcoat crazing and checking around the bolt holes.
To use this process for the ports I used my laminate trimmer and a 45 degree bearing guided bevel/chamfer router bit. The router bits guide bearing fits in the 5/8" hole so I used the laminate trimmer for those holes too.
On these ports, using the butyl, it is very, very difficult to tighten them down all the way at once. I tightened the ports over two days, which is short enough so my polysulfide sealant did not fully harden, but long enough to fully compress the butyl.
WARNING: I differ from the NFM instructions on this particular procedure. NFM says to tighten over a few days letting the sealant harden to form a "gasket" so you make your own choice on how to seal the ports but here is my explanation of why I do it the way I do:
I've been bedding fittings, tighten once or before the bedding is dry, this way for a very long time and never once had a re-leak. The idea that tightening a fitting all the way down squeezes out all the sealant is just not true. Take for example the aluminum valve cover on the Volvo 5 cylinder engine used in the V-70 series and others. This valve cover uses no gasket and only a thin layer of Permatex (Silicone) is required to seal it. You apply the Permatex, install the valve cover, and torques the bolts. Valve cover gaskets are under positive crank case pressure and deck fittings or ports are not! I have used the above method (bevel then tighten at once) on underwater fittings as well and still never had a leak.
Again, it's your choice as to how to seal your ports and I'm merely telling you how I differ from the manufacturer on this one point.
EDIT: If I had to do this job over again I would NOT use the NFM black butyl tape and would instead use Bed-It Butyl Tape in gray. This will completely avoid the need to use both a sealant and butyl. The gray Bed-It Tape is far less messy than the black tape from NFM.