Consider the nature of the square wave signals.
You seem to be looking to the fundamentals, which is
for linear small signal type systems.
But every digital edge presents a current impulse to
the system, times two per cycle, so a 3M clock can
make 6MHz tones.
Conversely your reference clock might very well be
used, divided down, to run internal logic stuff and the
"heartbeat" will get all over everything.
Phase-lagged clock perturbations can contribute to
subharmonic behaviors through bondwire coupling,
a ground-bounce that happens at just the wrong time
to advance / retard / advance the edge transition
from the outside world, etc. Placement of the RF
inputs, segregating them inside ground cages etc.
is desirable. Same concerns apply to the test setup.