The direction of the end stop is set in the firmware of the printer. Even with different setup end stops, you should be able to get a correct coordinate system without mirroring axes in slicers. This would be the preferred method to fix your problem!
E.g. my Ultimaker 3 Extended homes the Z on Z max having the platform at the bottom of the machine, a calibrated offset determines the actual Z=0.
Not knowing which firmware you are using, in e.g. Marlin Firmware this is set by code lines in the file Configuration.h:
// Direction of endstops when homing; 1=MAX, -1=MIN
#define X_HOME_DIR -1
#define Y_HOME_DIR -1
#define Z_HOME_DIR -1
Your end stop triggers at the maximum of the Y axis, so you need to configure it as a MAX end stop, i.e. use the Y_MAX pins by defining (search for the Endstop Settings section, note to also disable the YMIN endstop):
//#define USE_YMIN_PLUG // This disables the YMIN endstop
#define USE_YMAX_PLUG // This enables the YMAX endstop
and change the homing direction (Y_HOME_DIR) to 1:
#define Y_HOME_DIR 1 // This tells the printer where the endstop is located: positive for YMAX direction
Otherwise when used at Y_MIN endstop and the homing direction set to -1, the axis is reversed as you experienced.