It really depends on what game are you referencing to. Some game does require to add milliseconds (if necesary) to give the "exact" time runs as it should be (best example would be Minecraft short categories & any other game that has built in ingame timer).

Regarding the "counting frame", it really depends on how you do the runs & how you submit the runs. A basic example would be the framerate of your video submission, as 60fps has a different time counts as with 30fps or even 25fps (cmiiw). if you still unsure with the timing method that the game mods were used, feel free to ask the respective mods for further info.

This post seems familiar. https://www.speedrun.com/speedrunning/thread/1alp2/1#ycbtl