How to calculate MySQL Transactions per second
BEGIN; INSERT...; INSERT...; COMMIT; = 2 inserts, 1 begin, 1 commit.
SET autocommit = ON; INSERT...; = 1 insert, 0 commits.

I don't see any way to get the 'right' answer of '2 transactions'.

However,


if your code always uses BEGIN...COMMIT, then you might use Com_begin as the number of transactions.
if your code never uses BEGIN...COMMIT, then you might use Com_insert + Com_delete + Com_delete_multi + Com_replace + Com_update + Com_update_multi as the number of transactions.


(I consider autocommit=OFF...COMMIT to be an abomination.)