The line-by-line production may not make the best use of
a) object-oriented design principles,
b) other Java idioms.

That could negatively impact performance, especially if the "identical
results" included copying any bugs.

Java also has multiple optimization options relating to hotspot compilation
and garbage collection.  Realistic benchmarking would require simulating the
typical data load between the two versions.  What is typical?  That is
non-trivial, as is the game of simulating it.

Also, Java's architecture favors long-running processes within an established
JVM; JVM startup is a significant time eater.

A third contender should be a Java rework of the original algorithm rather
than the original code, or possibly a substitution of a better algorithm.

The problem here is to give the customer information that will actually
benefit them, and products that actually serve them.  Coughing up a meager
translation of a FORTRAN program to Java, then running meaningless benchmarks
to try to figure out if you did anything useful is a huge disservice to your
customer.

Make sure the benchmarks measure something that has actual importance, and
make sure the work has real benefits to the customer.