After homing X & Y (stage 9 step 18), I lowered the gantry as instructed and noticed the center of the probe is pointed 2-3 mm off the back of the platform when Y is homed. Thus it cannot trigger unless it is a few mm out from the end-stop position. Is this correct? Will the machine ever need the sensor in this position?
The nozzle is aligned correctly, so perhaps I'm just being overly cautious here.

Z-safe homing is enabled by default. It is responsible for two things, making sure that X and Y are homed before homing Z. Moving the probe to the centre of the platform before homing.
any tips on setting up? safe homing is not a setting you can just enable from what I can tell... and the nozzle is just mushing into the bed and flexplate whenever I run home, is there settings you can suggest? I at my wits end and im so close to being done...
Okay, good. Thank you.
First, make sure you enabled Z_SAFE_HOMING in Configuration.h. This setting causes the printer to home X & Y and then go to the middle of the bed to probe for Z. Secondly, in Configuration.h there is a setting named NOZZLE_TO_PROBE_OFFSET. It should have already been set by Makertech. The value for X should be a negative number. What this does is tell the printer that your probe is to the right of the nozzle. When it goes through the ABL procedure it will use that value to offset the print head so that the probe is over the place where it wants to check.
So to answer your question, when you home X & Y the nozzle is in the correct position in your picture. You'll be fine when you home Z.