I think I know what you're getting at. Binary is designated by 1's and 0's. The number of possible combinations that can be produced by a particular number of 0's and 1's is determined by 2 to the power of however many "binary numbers" you have. Again, "binary numbers" is defined by the number of "1's and or 0's".
I believe the original Nintendo was "8 bits" (or had 8 "binary numbers"). Which means every command it could process was "2^8" which means there are 256 different combinations or different communications that can be processed in a single command. 4096 different combinations works out to "2^12" (or 2 to the 12th power).
Significant computer numbers, therefore, are typically, 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, 16,384, 32,768, 65,536, etc.
4096 Fits that pursuant to the programming that the program may be limited to handling the commands from only that number of units at any given time as there are only 4096 different combinations that it can use to represent a different unit on a programming level when considering commands from them. I totally understand it, but it is still appropriate for Blizzard to clearly communicate the details of that to us players/map developers.
Note: I did create a map in the galaxy editor with well over 4096 units in it owned by different players, but I didn't run the map so I was not able to tell whether they could be issued commands, but I think based upon our experiences, that the unit may be able to exist, but cannot have commands.