Agile's teaching of "thin, vertical slices" doesn't apply just to features.
Organizations move forward in thin vertical slices too.
Story mapping teaches us to do incremental, value-first programming and integrate the "threads of functions" all the time from end-to-end.
CI teaches us that integrating thin slices frequently avoids pre-release integration nightmares (and post-release nightmares).
Likewise, we leave room for learning and growing, because what we learn in iteration N may give us different options and opportunities in iteration N+1 and onward. We have an idea of where we want to go, but we are always seeking best value.
However, too few agile transitions are done in an agile way.
It's only reasonable that a pre-agile company would want a waterfall, Big-Design-Up-Front plan with staffing and milestones for an agile transition. But we, as post-transition coaches and consultants know better and are supposed to be giving advice and support.
And just when we're building software, building a transition in bottom-up, architecture-first, isolated, horizontal layers causes a lot of integration problems.
We shouldn't act surprised.