Either way, the properties are only changed for the tracker itself; it won't really affect the NSF or NES files you output because the properties in FamiTracker only affect FamiTracker itself.
Imagine an actual NES or a Famicom; picture yourself swapping the crystal oscillator from the machine to something faster or slower. This is essentially what you're doing to FamiTracker when you change the properties. As for exporting ROM files, all you'd be doing is creating Assembly language code for the 2A03 to run; it has no effect on the console's operating frequency.
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