Noise on the autotune isn't the end of the world / isn't something to worry about. Only if the noise is nearly as big as the actuation is there a problem.
In general, leave the filters alone.
Especially the "hardware" filters-- I never touch those, they are a sufficient antialiasing filter.
For things with very large props where the prop frequency can get in through the 55Hz filter, it can be worth changing the cutoff order and frequency-- e.g. to a 35Hz 4th order filter if the blade frequency is 55Hz. This is pretty much the only time it's worth tweaking. For smaller things, you're better off with mechanical filtering (damping).
The autotune parameters just control how aggressive of PIDs you get from a measured system, and the defaults are almost always fine.