It is my understanding that the incident that Vilas alludes to (or at least one extraordinary similar) was a product of more than just a knee jerk reaction to changing SOPs.
The airline was relatively new, and apparently had largely been set up by people who were from a major airline that went out of business a few years prior. That defunct airline had a reputation of reinventing the wheel. Apparently in the old airline they had completely rewritten the entire FCOM to the point it barely resembled anything by Airbus. I have been told several old stories of crews happily pulling A320 CBs to resolve ECAMs leading to near disaster at one point. This "we know better" culture seemed to manifest itself in the new airline with the old folk - resulting in moving those annoying non Boeing-like FMA callouts somewhere unobtrusive.
There are also legal systems in some countries that could cause the NAAs legal headaches if they have knowingly let an airline deviate from the manufacturer's SOPs and a disaster happens attributable to that change (like the aforementioned GA event).
Once the content of this thread grew some manners, it clearly shows no one differed from the concern of the OP regarding companies' deliberate variations to the manufacturer's SOPs.
As a side note, however, it must also be said that some of the manufacturers are less than fully proficient at telling Airlines of all of the changes. I found one the other day (admittedly small) that had crept in - and the new procedure was completely contrary to the specific advice received from the manufacturer on that very procedure about two years ago.
Finally, if your VS is already averaging around 1000’ a minute or less why would you mandate selecting vertical speed?
You wouldn't
mandate the selection of VS. You'd expect the pilot on the day to use the most appropriate mode to achieve this. The 1000 foot ROC/ROD is mandated in AIPs in several countries so pilots are duty bound to comply. In any case focussing on this example is misleading as it's not really against the Airbus way. There are various modes for changing height and one would use the most appropriate one for the day.
There are other far more glaring examples that illustrate the Manufacturer SOP deviation much more clearly and with potentially significant consequences.