The risk of running out of infielders, though, is present on every pop-up to short left.
I'm not disagreeing with your analysis, and perhaps Marrero is better rotting on the MLB bench while Castillo gets ABs in AAA.
Anyway, I do think you're in a bit of a swamp with the "no IF" scenarios, at least as far as they relate to PH. I agree it's a real risk, but I still think it's not a very large one.
First, there's the mutual collision scenario you floated where a couple of key guys hit each other so severely both can't continue in the game. That happens what, once a year on average, or less? I mean, it's a bad year if it happens once, and freakish if it happens twice. But to create an IF shortage the collision has to be Holt/Xander mutually injured, or Holt/Pedroia mutually injured. If one can continue, the injury does not matter, given that an uninjured Holt moves to the IF, or Castillo replaces Holt. If both are injured Mookie comes to the IF, and Castillo gets in the game. If it's another IF and Holt, Ortiz can do a couple of innings at first, etc. The point is, someone would continue.
Anyway, the mutual injury collision game isn't a guaranteed loss, just because a collision occurs at some point during the game. But chalk it up as a loss if you like. But assume replacements arrive in time for the next game. (Unless we're talking about a mutual collision in the first game of a double header on the west coast.)
Second, there's the "Holt unavailable due to any kind of injury/PH, *and* one of Xander/Pedroia injured during that game" scenario. I mean, we're not talking about one of them being on the DL - we'd get a replacement. We're talking about the chance of mutual injury, or Farrell messing up the PH (far more likely). To prevent that, the rule should be that Farrell should never PH for Holt until the 9th.
In any event, the same swaps as above apply. Again, not an automatic forfeit, but call it a loss if you like. That might happen, on average once a year? Twice?
So, it's a real risk, but not one that's going to happen with any kind of frequency. Also the first time it happens, I think you'd see a roster correction made to address it. Or the roster will be changed anyway due to injury, trade, etc.
We shouldn't be talking about discontinuing offensive platoon use over, at worst, 2-3 freakish injury driven losses.