The plugs being switched won't matter. Each voice coil has a positive and negative terminal, the factory plugs won't let them get reversed.
I can't tell you if that sub will fit for sure, I assume it would though. But I will say that on my 09 the terminal polarity was not marked. so if yours also is not and you want to run a aftermarket sub off the factory amp, you can do the fallowing: use a AA battery to determine the polarity. Use some spare wire and electrical tape a lead onto the + and- of the AA battery. Then touch the leads to the voice coil terminals on one voice coil. The speaker will thump each time you make the connection. If the come is moving outwards, then that is the correct polarity. Do this for each coil to be sure. Based off knowing the polarity of the voice coils you can determine the polarity of the factory plugs and label them, cut off the plugs and attach the leads to your new in the manner of your choice.
Hope that long winded shit helps someone one day
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