How to make struct align in PIO?

typedef struct
{
uint16_t rtcYear;
uint8_t rtcMonth;
}SensorT;

typedef struct
{
uint16_t rtcYear;
uint8_t rtcMonth;
}timerT;

and should I add the align between every struct or just the top and the end?

The question should not be “How to make struct align in PlatformIO” but “in GCC”. The only thing that matters here is the compiler, not the whole build system. For setting struct alignment, see official GCC docs Type Attributes - Using the GNU Compiler Collection (GCC).