Hello Viking01, and welcome to the forum.
In general, when a peripheral module is enabled, it will over-ride GPIO functionality. I suspect this will also be the case for the input capture pin.
I think that you mean the TPMCNT (16-bit) register, compared with the TPMC0V register.
An input capture event will write the current contents of TPMCNT into the TPMC0V register, at the instant of the event. Interrupt latency may then cause the two values to slightly differ at the time the interrupt is processed. The true timer value for the capture event will therefore be that within TPMC0V.
Regards,
Mac