PA15 is reserved for SPI3 NSS.
Timer 2 ch 1 is not mapped to PA5 to allow to be used as SPI1 SCK.
In the same context, PB10 and PB11 are reserved for (SPI2_SCK or I2C2_SCL or UASRT3_TX) and (I2C2_SDA or USART3_RX), respectively.
So Timer 2 was given lower prio versus I2C2/USART3, because there are plenty of other timers available on other pins.
Same applies for other pins you mentioned, in favor of SPI, I2C and USART.
Take a look into generic_f407v.h for reserved pins and what are they reserved for.
To activate TIMER2_CH1 on PA15, PA15 must be mapped to the respective alternate function AF1, which is not done in the current version of the repo.
You can use the function gpio_set_af_mode() using my repo.
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