Are you interested in receiving the instructions correctly, or interested in how the instructions are executed by the hardware? This answer doesn't go into the software communication between controller board and software that sends the instruction from another software/hardware platform (see this answer), this answer addresses the positioning/movement.
Most of current 3D printers do not track the position of the print head. The software instructs the head to go somewhere, but it never checks if it actually arrives at that exact position. Problems like missing steps of the stepper or skipping notches on the belt are not detected and the printer will continue thinking it has reached the position.
Skipping of belts is a mechanical issue and should not occur (nor can be detected unless there are stepper steps missed), but skipping of steps is something that can be detected by certain type of stepper drivers (trinamic). Steppers do not use a feedback loop to check the final position. Servos, opposed to steppers, use a feedback loop, and as such are able to reach the position as instructed, but this comes a an increased cost, servo's are more expensive and hence not found in most of the "cheaper" 3D printing machines.
It is up to the designer of a 3D machine to choose the motors for the positioning system, if it is not highly loaded, you go for steppers without a feedback loop, or in higher loaded machines for servo's (basically steppers with some positioning electronics for the feedback). In case of a stepper you hope that it reaches the destination you tell it to go to, for a servo, you known that it reaches that exact position.
To get back on topic of your question, there is no feedback on reaching the position (you call this acknowledgement), you just send the G-codes sequentially or in a buffer to the printer electronics which executes the statements one at the time (this is done by the firmware, this this answer for replies of the machine on the code it receives). It is your choice of the hardware that actually determines whether this is executed like instructed. Do note that most machines are not highly loaded (the 3D printhead is not very heavy and normally does not hit any obstruction in its path as Z advances) justifying the use of steppers without the need for feedback. CNC machines, certainly the larger ones, that position a highly loaded cutting tool need such a feedback loop as the positioning needs to be very exact. You need to consider the forces at play in your paper punch machine, but from my point of view, your machine does not seem to be highly loaded. In such a case you are not in need for a more expensive positioning system, nor the need for the processing of a return/feedback signal in your custom software.