Z axis not retracting full distance

For threaded rod, 7.5 seems too fast to me for a max feedrate. V1 suggests a max feedrate of 8mm/s for a 4-start lead screw. I’m not sure of the movement ratio between a 4-start lead screw and the threaded rod, but I’d think a max feedrate of 2.5 would be more appropriate for threaded rod.

I’m not sure what version of Marlin you are running, but in the later versions the max feedrate can be set both by g-code ( M203) and from the display. If you can easily set the max feedrate, I suggest you dial the number down and repeat your test. Pass or fail, the test will tell you something significant.

As for Fusion 360, if you are using the free version, I’m not sure it will honor your plunge rate. For the free version, they removed rapids and have Z move at the same rate as X and Y. Don did a rewrite of the postprocessor that has settings to mitigate the issue.

As mentioned above, if it turns out to be a feedrate issue, and if the slower speed is an issue, there are a couple of other things you can try to address the problem.