Looking at your prints, the problem is possibly related to the fade out height of the BLTouch functionality.
If you look closely at the 20x20x20 mm cube:
half the print is fine (top half of the original correct cube)
the bottom "half" (not really half as it is stretched) is porous (grey, indicating more space allowed than the correct layer height ...
No, settings are stored in memory (or the equivalent storage location).
When a new firmware is uploaded, the values set in the newly configured firmware can be set by Restore Defaults from the Marlin printer LCD the user interface. Alternatively, you could print a G-code file containing M502 and M500, or send them over using a console.
Reset all ...
Using a larger carriage will, if too large, diminish the printing area.
To determine the correct values (for the X-axis) you:
First need to assure that the nozzle can reach the origin, if not, try to see if you can move the endstop without the carriage hitting the frame, if not possible, your left margin will be decreased. If there was enough ...