Hi Giles,
That does sound as if the start-up linking capability of E3 could provide the composition mechanics you miss - just inside the container image. Doesn't it?
E3's dependency resolving and version management is not needed - in the container you want one set of modules. But every instance could choose which modules to use - which is configuration, supplied from outside the container.
The Generic IOC image could provide all the generic Device Support modules, and the second layer of images could provide additional modules, like extension packs. Done by application, by institute, by lifecycle or any other criteria.
Interesting...
~Ralph