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The 5.2 xntp3 RPM, despite being happy to set the kernel clock and track time and stuff, does not actually appear to use the kernel-level PLL facilities. For example, adjtimex --print will report 'status: 64' (clock unsynchronized). Among other problems, this will cause the kernel not to update the hardware CMOS clock every so often. This will in turn cause a machine to potentially jump a lot of time when rebooted. The best cure for this appears obscure to me, unfortunately. I have become lost in a twisty maze of source RPMs and autoconf.
Running Red Hat 6.0 with a 2.2 kernel, adtimex --print reports status: 1 (PLL updates enabled), so the PLL code appears functional in 2.2 kernels. Setting the CMOS clock can be done within xntp, but is not an essential part of xntpd functionality. Since xntp3 syncs to reference clocks quite well even without the PLL code, you can set your CMOS clock manually with other utilities whenever xntpd shows an acceptably small offset to a reference clock.