the fire (yellow glow light with smoke) started in the vicinity of the MCU's internal regulators pins, which are just on the side of the oscillator pins.
This is why labratory power supplies have a current limiter...
You have a very strong short, most likely a VCC pin connected to GND or a GND pin connected to VCC. Shorting a GPIO usually does not (much) damage because of R_DSon in the GPIOs driver. Triple-check your schematic an layout for errors with power pins.
Two crystals running at nominally the same frequency on the same board is a recipe for interference, especially if the interferer is a logic circuit with fast edges.
In this case, your RF circuit won't cause any problems for your MCU, but your MCU will certainly affect the spectral purity of your RF component.
There are several options.
1) Build it and see if the interference is permissible. This is difficult, as you don't know whether you have the worst case for any test. You would need to sweep the frequency of the MCU crystal through a range above and below the RF crystal. However, even if you arrived at a conclusion that the RF signal stayed in specification the whole time, it might not on the second board, or after a board modification, or at a different temperature, or with a faster process MCU that has sharper logic edges. Making sure a given setup that could cause problems doesn't is a long and difficult task.
2) Phase lock the two crystals together, though that is more complex than ...
3) Only run one crystal, the RF one, and buffer the signal across the board to be used by the MCU when it needs it.
I can't imagine how running one crystal with buffered switchable output(s) would take more power than two independent oscillators.
Best Answer
No, the polarity does not matter.
Crystals do not have a polarity.
Watch out with Crystal oscillators in a similar housing though (also 4 pins) as their polarity does matter.
But since this is a crystal only (no oscillator) polarity does not matter. It will work mounted either way. I speak from experience with similar crystals from the same manufacturer.