The general idea, i.e. that applications be programmable, is laudable. I'd wish there was some way of making this happen "in principle", I really do. There is actually sci-fi which makes this a reality - a common programming model - but this is not, currently, reality.
Unfortunately, software being what it is as of now, achieving a general solution to this is impossible. ATLAST is no exception to this, being a component targeted at a specific language and system. There are hundreds of such implementations - I did some myself - but each one is just the n+1 implementation of said concept.