Perhaps a clarification of that term is needed. "Runtime" does refer to the time when the program is running, but when talking about included files, it's usually short for either "runtime system" or "runtime environment". When any program is run, the executable does the basic setup for the type of executable it is, followed by loading anything that the executable lists as required to run. Usually some of what's required is included in the OS's files, especially the "kernal", but not all of what's required.
To give Pico-8 as an example, this game I exported with version 0.2.1b a while back has a windows distributable that includes the optimized .exe file, a data file, and a mysterious version of SDL2.DLL. Since the .exe file loads the DLL file at the beginning of its runtime, it would be counted as part of the runtime environment. Thus, the game's file size is the total of all 3 files, not just the game data and the exe file.
Also, I'll go ahead and mention that the pico-8 IDE is too big (around 20 MB) but it looks like a windows distribution is only 2.83 MB on disk, so you should be fine using pico-8 as long as you export a stand-alone distribution rather than the cart (look up export in the readme if you don't know how). More generally, if you're not sure if a file is part of the runtime, move it out of the game folder temporarily and see if the game runs without it. If not, it counts.