Good Question. Sorry I cannot really answer your concerns.
the manufacturer's recommendations are just that, Recommendations. If the company decides to implement some other way of doing things then they will be responsible if the deviation from the recommendation directly causes an incident/accident. the deviations operators make are therefore usually more conservative.
using autobrake for all landings is safer than not doing so as there is less chance of a pilot related error during the braking process. It's much easier to explain your actions during an inquiry if you can prove that you followed SOP (when it was safe to do so).
and by the way if the company is spending too much money on tyres they'll just cut our salary to pay for it so nothing to worry about.