There's actually a really slight effect when MW+II isn't running, but it's so minor that it's not really anything to worry about.
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3. Modification of the SCC clock from 4MHz to 3.672MHz. This one is pretty simple! The stock Lisa clocks the SCC at 4MHz, but the PFG changes this clock to 3.672MHz (the same frequency as the Mac Plus SCC) for better compatibility with the Mac serial ports. Unlike the other two upgrades, this one is actually active all the time, even when you're running a different OS. This has never seemed to cause any problems, at least from all my testing, but I think it's definitely worth pointing out that the PFG does at least slightly change things when running other operating systems!
More details:
The Lisa's SCC has two sources of a baud rate clock, the "P Clock" and a crystal.
The crystal is of a frequency that facilitates baud rates with 0% error but it is only available as a baud rate source to the B port.
The P Clock is 4 MHz in the stock Lisa, which results in errors of about 0.1% when programming baud rates up to 19200 -- See "Figure 2-10 Serial Port Baud Rates" in the Lisa Hardware Manual.
The Mac uses a 3.672 MHz P Clock which gives baud rates with 0% error. The Mac does not have a separate crystal, so P Clock is used to generate the baud rate for both serial ports.
When designing the PFG, the choice was made to set the PFG's P Clock to 3.672 MHz so that the Mac software that directly accessed the SCC hardware would work properly.
So with the PFG installed, Serial B will work correctly with Lisa software that uses the crystal as the baud rate source, and both ports will work correctly with Mac software that uses P Clock as the baud rate source. However, Lisa software that uses the P Clock as the baud rate source for Serial A will not be generating the correct baud rates.
Due to the baud rate error that results from using the 4 MHz P Clock in the stock Lisa, it is preferable to use Serial B (especially at higher speeds), but in the event that you must use Serial A with early software (eg. Lisa Terminal), then you will need to remove the PFG (or adjust the baud rate at the other end to an unusual number to compensate).
edit: corrected magnitude of Serial A baud rate error and added reference to Hardware Manual