Warnings in SSP headers

We're using S5D5 board with SSP 1.6.0. When we add CTSU driver, r_ctsu_cfg.h header is added (generated) to the project and included to hal_data.h file which is used in the whole project. The r_ctsu_cfg.h file contains following code:

#if (CFG_AUTO_TUNE <= 0)
#warning "Initial and Run-time auto-calibration/tuning has been disabled. This is not recommended."

#warning "Initial baseline setup and Run-time drift compensation has been disabled. This is not recommended."

We don't want it so we have both disabled and 0. Which is BTW default in the configurator. In turn, it generates hundreds warnings in the whole project.

How to avoid the warnings? They're manual so I don't see an easy way how to disable them. We can make a copy of this header, fix it and put it in some include directory before the original one. But that's fugly and we'd have to check generated files for possible changes. Is there some supported way how to fix it?

Personal note: it is the strangest thing I've seen within last few months.