If you move up the end stop such that it raises the nozzle with respect to the build platform you lose height, so basically the answer is yes. But, as seen in your referenced question, your nozzle location is determined by the mechanical layout of the printer and the end stop had to be raised in order to print at all. This means that although you have less height to move the Z gantry, it can now actually print the full range the printer is designed for (the max Z to print is fixed in the configuration of the firmware of the printer and is always smaller than the maximum Z of the mechanical layout). Theoretically, if you ever make a lower profile hotend head, you would be able to lower the end stop and gain a little in height and adjust the firmware maximum Z height.
E.g. in Marlin firmware, for an Anet A8 3D printer,
#define Z_MAX_POS 240
in the Configuration.h file defines the maximum print height of 240 mm. If you would deliberately increase the Z end stop height and platform by let's say 50 mm, the printer thinks it still can print 240 mm, but in reality the gantry will crash against the top mounts and thus limit your printing height.