Surely there'd have to be two interrupts from the same source during the disabled window before you'd lose anything? Otherwise the interrupt just gets delayed until they're globally re-enabled. Looking at millis() for example, it disables them for about 9 cycles, or 562.5 nsecs at 16MHz. So worst case, if an interrupt fired just as they were disabled, that event would get delayed by 562.5 nsecs. Is the PLL code really that sensitive that it can't cope with 1/2 usec of jitter in the timer interrupt?
SNR = 20*log(1/(2*pi*f*t))
SNR = 20*log10(1/(6.28*1600*1e-7)) = 59.96