How to calculate total memory used by one table?
Both are correct; both say the same values.  (Don't divide by 1024*1024; it will be a little more obvious.)

In InnoDB, the PRIMARY KEY is "clustered" with the data.  That is, they are both in the same BTree structure.  The PK provides the order; the data provides the content.

In your table, the data is ~4GB, including the PK and BTree overhead; the two indexes are in two separate BTrees, adding up to about 5GB.