Your initial reasoning is correct, which is why it's best to first bring the water to boiling temperature, _then_ drop the eggs in the pot.
Think about this for a second: When the water gets to 100C, it stays at 100C as long as there is sufficient fire under the pot, correct? So, your water is stable after it boils. You can then drop the eggs, time 5 minutes, and you're done.
If you don't do this, it would be difficult to apply a time to the process, like you said. But, if you let the water boil first before adding in the eggs, it's always going to be 5 minutes to soft-boiled eggs, so it becomes easy to time the process.
Think about this for a second: When the water gets to 100C, it stays at 100C as long as there is sufficient fire under the pot, correct? So, your water is stable after it boils. You can then drop the eggs, time 5 minutes, and you're done.
If you don't do this, it would be difficult to apply a time to the process, like you said. But, if you let the water boil first before adding in the eggs, it's always going to be 5 minutes to soft-boiled eggs, so it becomes easy to time the process.