Change Slic3r settings for left handed coordinate system
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
// :[-1,1]
#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.