Hi nilesh,
they are unrelated because the different layer they need to work with (MTU layer 2 vs TCP layer 4) however, you need to pay attention to let these to values to work together to avoid excessive fragmentation or retransmissions due to a too big segment vs some limits to the MTU.
Although they should not have impact on BGP, i would enable neighbor transport only with an outage of at least 30 minutes planned. Never challenging BGP
HTH
Alessio