Without getting into whether or not an injection of water/methanol injection is the "same" as 100 octane race gas (because it isn't - different length hydrocarbons and other differences), I will say that you can run 92 or 93 octane fuel on a 100 octane map with water/methanol injection.
Keep in mind even though it is a performance tune Mopar is still leaving some level of buffer with excess fuel and a bit conservative timing relative to say if you had your engine tuned on a dyno at the edge - that factor should provide you with even more comfort.
Properly implemented you will not experience knock and any knock learning the reprogrammed PCM has will permit it to run maximum advance. There is no reason that with your system and the stage kit that you shouldn't get the performance results of the tune from pump gas.
I would look into a variable flow kit though. I used dual and tri stage kits for a long time due to a lack of alternatives and it does work, but the difference with a true variable flow kit is night and day.
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