Curios question Davd;
I've found that a single-page InDesign file built for smooth scrolling can be a curiously flexible design. Let's say your ID file is 768 wide and 3000 tall, you can export that to an tablet dimension, and then export the same file to an phone dimension. These article files will scale to fit a device. So if your project has two top-level nav systems, you could have a set of tablet collections and a set of phone collections, and then you could load the two article files into the matching system.
The result would be one design file --> two article files --> that become content for two articles. Maybe an easy way to cut down on your design files, as long as smooth scrolling pixel-perfect articles is going to work for you.
As for the color conversion, it depends on whether the image is resampled in the export. All the old patterns of non-interactive and images in slideshows and scrolling frames apply here. Same deal for pass-through overlays -- they'll pass the asset right on through without conversion.
HTH