The way the Rust game calculates heli HP and decides if it is killed or not depends on maths within the game code which is based on percentages of rotor health against overall HP. Try to use the default values as a guide to creating more reliable custom settings. For example, the default "Easy" heli in my plugin is the same as the vanilla patrol helicopter in the game. The vanilla HP stats are:
10000 Main heli HP
900 top rotor HP
500 tail rotor HP
If we do the math:
Top rotor: (900/10000) x 100 = 9% of total HP
Tail rotor: (500/10000) x 100 = 5% of total HP
For the heli damage to function as you expect you need to keep these % ratios, or the built in game code calculations are wrong, this is why you are seeing this discrepancy. So whatever you decide is your main HP is, let's say 100,000 as in your config. That means the main rotor HP should be 9% of that, which is 9000 and the tail rotor HP should be 5%, so 5000.
I should probably add that info on the plugin page for everyone to know.