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I have installed custom ROM, Official Lineage OS 14.1 on my Redmi 1S. I used to reboot device sometimes. And, I noticed that each time after reboot, battery percentage reduced by 2%. I also, tested on my Redmi 3S, running stock ROM, But, there, it won't drop battery. Does the device really use 2% of battery to reboot?

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Yes and no

It does take energy to reboot, but it isn't the phone rebooting that takes this energy. The energy is lost through hystersis which the battery algorithm is accounting for.

Krexington_III, who worked for a summer as a fuel gauging engineer for a major cellphone manufacturer in northern Europe and says:

Hysteresis is simply the fact that once we've got the battery discharging, if we stop discharging it (say, by turning the phone off), it will keep on discharging by itself for a short while.

(Paragraph 3)

https://www.reddit.com/r/explainlikeimfive/comments/1qrdc9/eli5how_do_digital_devices_know_how_much_energy/

Phones need time to tell how much energy the battery has, and don't keep track of the battery while it is off. Your phone was programed to estimate that 2% was taken away while the phone was off due to Hystersis. Your other phone does not make this estimation (the user won't notice).

I suggest reading Krexington_III's post for (a lot) more information on how phone batteries and their algorithms work.

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