From an user point of view it would certainly be more pleasant when Prestools would use the TB login. However, it is not as easy to implement as you suggest and it might have disadvantages too.
Prestools operates outside the TB engine. Only that way can it have complete control over the screen and achieve adequate speed. So in order to use the TB login - that is tightly integrated with the rest of its code - the code must be replicated without that context. That would require a deep understanding of how the TB login works (the shop password is stored encoded and you also need to deal with the cookies that keep you logged in). So this is quite a tough job and I have never found the time and motivation for it. Maybe somewhere in the future, but this has not a high priority.
I believe Prestools is quite secure as it is. But of course suggestions for improvement are always welcome.