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This is the CMSIS device definition (header file). When you undef in setup it is local to the cpp file (.ino). Even if you disable it globally, I do not advise as it is probably used by LL/HAL source files and CMSIS one.

Finally to answer your title question, no it is not possible. The only way is to use HAL_TIM_MODULE_ONLY to globally disable the usage of the HAL_TIM_MODULE by the Arduino API level.

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