Update: I found a nice article about chocolate printing: https://all3dp.com/2/chocolate-3d-printer-all-you-need-to-know/
You are searching for chocolate extruder. I did not find one, which would fulfill all your requirements. You have to adapt each solution.
Zmorph3d Liquid paste extruder
According video ...
The Y-Max setting does not help, because it is the software end stop for the other end of the axis.
The Y Home position also doesn't help as it only changes the coordinate that the printer assumes for when it hits the home position. That is used for printers (like deltas) that home to the max end switches.
What could help is a little bit of G-Code right ...
Now I've finally had time to look into this, since I knew it somehow existed, but wasn't sure how it worked:
Use the M206 G-code command in Marlin, Sprinter, Smoothie, or RepRap Firmware to offset the 0,0,0 coordinate of your printbed relative to the endstops.
The reprap.org wiki page says:
The values specified are added to the endstop position when the ...
For your application, you should 3d print a positive model, then make a silicone mould negative of that model. Then use the silicone mould to make the final chocolate. Clean the silicone thoroughly before initial use. Fill gaps in the 3d printed model with a light epoxy resin. Use mould release and ensure you wash and sterilize that silicon mould before ...
In my experience, direct printing of chocolate is tedious because:
It has to be around 88 C to melt; and
It doesn't solidify very quickly at normal room temperature.
Unless you can print in a chilled environment (freezer is better than refrigerator), you will likely wind up printing a chocolate puddle. Even then, you have to heat not only the reservoir but ...
Cura contains a few different so-called "special modes" which changes what the software does with your STL. One such special mode is Mold mode which, instead of recreating the object, creates a mold for the STL. It appears you may have that setting turned on, so disabling it will cause Cura to work as intended.
To answer your other questions: