I haven't found a way to do something like this. If you're automating, you eventually are forced to use blockinput because if you use the mouse or keyboard you're going to directly interfere with whatever you're trying to do. You need mouse in X,Y position? Move your mouse while this is happening and it won't be where you need it. Automating while doing work yourself isn't something that autoit can do.
Maybe a virtual machine would work, but i have no experience working with it. I don't think it would work.