It would be unexpected in both directions - in fact I can more easily see "why is flexible layout changing my expected values?" being a question if you're expecting to do hand-made animations through hype's runtime in a specific manner.
Take CSS for example, if you have a font-size of 12px and then set a scale transform of 150%, you wouldn't then expect to read back a font-size value of 18px. It is really a matter of what space makes the most sense to work from.
There's a few principles on why the API is this way:
1. getting and setting need to use the same values; often a flow is to read a value and set it to some multiple. If the get and set are inconsistent then programming is near impossible
2. direct access to the Hype runtime
3. easy conceptual model to control items
4. low filesize footprint
I do think it makes sense to allow both modes; the main reason this isn't presently an option is #3 - an extra mode is extra learning - and not every document needs to be concerned with flexible layout, and #4 - being able to do a set requires converting the flexible-layout space back to hype's canonical space, and frankly that's a lot of code which doesn't exist in the runtime that would only need to exist for this feature.