There are two kinds of bonuss when it comes to speed.
- Booster. This increaes speed by a certain %. During the duration of the item.
That is, buy it for 1 hour, and during one hour, any building will be built in 25% less time. For example, a building that requires 1 hour and 40 minutes (100 minutes) will be built in 1 hour and 15 minutes (75 minutes).
This bonus is activated and stays active regardless of if you use it or not.
- Speedup. This deducts speed from the time it takes things to finish.
That is, if you buy a 1 hour speedup for somthing that takes 3 hours and 20 minutes, it will take 2 hours and 20 minutes.
This bonus is used directly and it's effect it's always instant.
In this case, when you choose 'instantly' you are reducing all the duration to 0 for that certain timer.
The only exception it's Transportation Speedup. It acts like a Booster.
It should be renamed to Transportation Booster, by the way.