Sorry this is a bit of a long one, hope it helps.
The NX standard flat port and the custom flat port are, in fact the same port, the only difference is once the body of the port has come out of the mould a man with a drill puts a hole in it to accept a manual focusing gear. So I expect the "nub" that needs to be removed is still on your port, but it sounds like a simple job to do.
The problem, as I read it, is that the fattest part of the 105VR lens, when mounted on your camera and fitted into your housing, is situated at the point where the ports are attached to your housing which is the narrowest point of the rear opening of the port. So I suspect that there will not be enough room to fit the focus gear because the gear will have to pass this point to mesh with the gear knob in the housings body
I have looked at a SEA and SEA port webpage here
http://www.seaandsea.jp/products/accessory/acce/port.html
there are two new ports that were introduced recently I believe thay have been especially created to house the 105VR lens, they are the DX PORT BASE, and the DX PORT 50 check out these new ports, they are not as big in diameter as the standard flat port and I am assuming that they will accomodate both the lens and the focusing gear, not exactly sure how they managed that not having seen them up close yet.
If you do not already own the standard flat port you may want to think about the custom port because I have not heard anyone saying that the focus/zoom gearing on the custom port interfers with the lens in any way. with the custom port you have access to manual adjustment on the port itself away from the tight spot at the ports base, check out my posting which may give you ideas on making your own (very cheap) focusing gear which meshes to the ports manual control. I've looked at a picture of the 105VR lens and the manual focus ring is near the front of the lens barrel, so a D.I.Y. Project could work well for this.
http://wetpixel.com/forums/index.php?showtopic=15291
I have used a Nikon 60mm macro through a flat port AND a dome port, both worked well, but there are several downsides to the dome;
The dome port is bigger than the flat port, making creeping up on your subject a little harder
You lose the slight magnifying effect of the flat port ( think about how everything looks larger underwater because your eyes are effectivly behind the flat port glass of your mask)
The glass of the dome port is much less protected than the flat port, so if you find some critter down a hole DON'T be tempted to push your expensive glass down there to get a closer shot.
The upside is, when travelling abroad you may only need to bring one port with you, saving weight and space. the dome port also allows more ambient light around you lens which will adjust your cameras meter readings allowing for better saturated shots.
What I am trying to say is that you dont have to put macro lenses behind macro ports.
I have not used woody's Diopters but have heard good things about them, as for the diameter sizing I imagine that there sizing includes the frame they come in and I believe the D.I.Y. Posting you linked to says that you have to remove the frame to make it fit. Check the diameter of the glass on your port to give you an idea of what size you need. You should post another question specifically asking anybody at wetpixel if they could supply photo's of thier D.I.Y. Fitting of a woody's to a Sea and SEA Flat port