The game Apotheon has a crash problem that happens with 100% of certainty during the run. Should we pause the timer when the game crashes? If yes, when it should be unpaused?
I don't think so in general. It is "real-time", so your final time is the amount of real time that passed between the start and the end of your run.
But, I think it also depends on the rules used by the community that speed-runs the game, if one exists.
Also, if it significantly impacts on the runner's ability to compete with other people who potentially have better setups than the runner does, I think that the timing would be done in a more fair manner.
Skyrim, Oblivion, Fallout 3, NV and 4, Dragon's Age, Deus Ex Human Revolution, you can find the leaderboards for all of those on speedrun.com. The livesplit load remover/autosplitter we use pauses the timer automatically when the game's process is closed. You can do the same thing manually.