Light- or Modem Sleep

Actually I do not interact with setTimeout. In the case of deepsleep it wouldn't make too much sense either I think, as after deepsleep the chip is resetted and therefor all timers are lost. In case of modemsleep it should be uneccessary as the CPU runs normal.

I am not sure about lightsleep (I did not implement that) but my current understanding is, that lightsleep needs an external trigger to wakeup:

Under the light-sleep mode, the CPU will not respond to the signal and interrupt from the peripheral hardware interface under the pause state. Therefore, the ESP8266 need to be waked up via external GPIO, and the wake process is less than 3 ms.
(Source)

To me currently it seems that there is no way where the ESP8266 could interact with setTimeout (however I am not completely sure when it comes to lightsleep as RTC is running according to the document above).