BJT Common Emitter Clipping
Why is it that the limits of the biasing/BJT cause a change to the
input signal when measured at the base of the BJT

If you try and &quot;brute-force&quot; the collector down to the emitter voltage, the normally reverse-biased BJT base-collector region becomes forward biased and the current gain plummets. After all, the base-emitter region is forward biased and, if collector drops close to emitter then that region is also forward biased thus ruining hFE.
The effect of this is that your base signal is now supplying a lot of the current into the collector and emitter and hence it clips due to the series resistance you have in the base circuit (Rsig).

The clipping at the high end is because it cannot swing above Vcc?

Correct.

the clipping at the low end is because the voltage at the collector
(V(n002)) cannot go below the voltage at the transistors emitter

Correct.