As it reads, yes, it costs a total of 3 IP to get an Improved Perk.
Two concepts behind this: (1) you need the "basic" version before you can improve it, and (2) the improved version is harder to learn.
That said, I think this is totally open to house ruling, and you should throttle it based on your group's preferences. For example, both the Perk and its Improved version cost 1 IP, provided they're acquired sequentially. However, for 3 IP, you can learn an Improved Perk straight away.
Cheers,
-Erin