For a 'full-house' CAE suite, I'd add a kinematics simulation package.
By the way, one of the most commonly used CFD codes (even used in F1) is open source.
Just like vehicle tuners, base engine designers rely on a *baseline* consisting of engineering 'rules of thumb', experience (especially the bad stuff), a bit of reverse engineering , etc. ... and then they "push the envelope" from there through experimentation with computer simulation AND hardware.
A good engine designer could design every component from scratch without a computer at all and be 95% right out of the box. The only trouble is, 95% fast enough is pretty much useless in a race!