Reference: p/n : Si5351A-B04486-GT
See here:
http://www.digikey.com/product-search/e ... 4486-GT%20
and
http://www.silabs.com/internal-apps-man ... dendum.pdf

So if practical for your project, consider to use this device with CLK1 to clock your XMOS device. This way, you should be able to leave PLL B untouched while configuring your custom clock on PLL A.
We can ping our local SiLabs FAE to confirm that the PLL A clock will remain active if working with only PLL B and vice-versa but believe our understanding is correct since the PLLs are independent of each other. In the past, have seen PLL vendors note the concept of glitch free transitioning from current clock to the new clock values but could not find such keywords in the Si531A documentation.
If you have the time, consider to source the very low cost Adafruit board (which is blank) and replace the PLL with the XMOS version to test these concepts.
The benefit of using the XMOS p/n is that you do not have to purchase any MOQ to receive programmed devices. For us, we have 24 Mhz on CLK0 so we will be sourcing in 1k pieces.