Hello Steve,
the procedure in the reference manual states nothing about switching sysclock to ref clock, but the INIT code does so, so you can't compare them. The INIT code is like using suspenders and belt together.
Regarding the method from the manual: I wouldn't feel good if I knew that my sysclock rides on some PLL settling transient, so I prefer to switch to refclock during a PLL change. Usually there is no time penalty since the PLL settling takes some time, anyway. Even with a 2MHz sysclock (the lowest allowed reference frequency), reading SYNSR takes only 6us. There is no benefit in "waiting faster".
The remaining question is, whether a too high frequency on the (inactive) sysclock multiplexer input hurts, or whether the RFD divider explodes while generating more than 80MHz <g>.
Regarding your guess about 180MHz, the manual says the opposite: according to the text, you _can_ multiply a 10MHz refclock by 18, that's 180MHz output from the PLL VCO. Obviously, you need to divide it with an appropriate RFD value to get an allowed sysclock.
The lower limit of the VCO output range seems to be 12MHz (3MHz * 4 or 2MHz * 6), that's a respectable 15:1 range.
Oliver