Hi Mike,
I can't talk about the brand name or the extra length of the casting but I can tell you about that push pin issue. The White car I bought from Kentucky arrived with such a situation and the owner had adjusted the pusher pin to compensate for (what I doubt he realized) was the fact that the pin wouldn't go all the way to the bottom of the cup in the master cylinder. I had White Post sleeve, put new seals in the cylinder and installed the unit. It seemed to work fine for a year or so then leaked fluid from that rear seal. I eventually found out that the cylinder was for a Volkswagen and used (if I recall) an 8mm pusher. The Amphicar has a 9mm pin. When you essentially jam the pin into the cylinder it prevents it from twisting a bit and puts slight side forces on the piston and seals so that the seal will fail rather quickly. I sent the cylinder back to White Post with an explanation of what was going on and they were nice enough to rebuild the cylinder again and replace the pusher cup with a 9mm unit at no charge. That fixed it and it has run fine for years.
You might call White Post and see if they will replace that pusher cup to you (they have a lot of spare parts there) or simply write off the experience and sell the cylinder on Ebay as a Volkswagen unit. Then get the correct one from Hugh. I wouldn't try grinding down the push pin, even though that seems like it should work because the curvature of the end of the pin would be slightly different from what it should be.
Regards,
John Friese
67 White
67 Red