I have not operated for many companies that have followed the manufacturers recommendations for flight operations to the letter. Most if not all flying training organisations where I've instructed used their own generic check list and procedures handed down over time and incorporated into the Ops Manual, CASA approved. Nothing much has really happened as a result, the issue would only be if you tried to pursue the manufacturer over a problem you caused. As a pilot you get hung for not following the company ops manual and CASA flight rules, the company is responsible for whether the ops manual is correct.
From what I understand the Malibu and Cirrus engines are recommended to operate lean of peak in the cruise. These are relatively new aircraft and may be an indication that the manufacturers are changing their tune.
I would say if operating the engine the way the APS guys say did so much damage then they would have been sued out of existence, especially since their main domain is in the USA.