1) If you look at the sleeve the pin is located into, you will find two grub screws, and by slackening them off, you can rotate the pin holder so that it doesn't foul any more. Your vernier adjustment sight lines will end up in a slightly different place. BTW, if you need to do any accurate indexing at all with the RT, you shouldn't be retracting the worm anyway. In many, many years of use, I think I have only ever retracted mine a couple of times until recently, when I gave it a strip down and mod. Even when outside clocking, I turned the handwheel., much more accurate.
2) You have a choice, a very heavy RT where they thicken the vertical baseplate to allow a full depth fitting, or by fitting an extra lug where you won't have the option of vertical mounting. You should do as everyone else does and has done for more years than I care to remember with Vertex RT's, make do with what you've got.
I will say one thing though, the Vertex is easy to mount, some others are a lot worse.
Boga