I wouldn't worry too much about it, I suspect things might move slightly, but not quickly or catastrophically.
I think the best advice I can offer based on my experience is to try and make your track base so that it will allow for movement, which may mean in your root case having the sections of track base either side of it less "monolithically" founded so that any variations spread along the track rather than concentrating in one place.
Your cable trays are a really good idea I think, as they will cope with and allow for movement,
One thing I would be wary of are bridge sections, only put them in where and if absolutely necessary as it is here that I predict you will see movement. As regards your roots, I'd run track base straight over with no bridging.
The great thing is that you are actually doing it rather than just thinking about it, the pleasure you will all get from your line will far outweigh any future issues - movement, bird poo, slugs, rain, I expect there are others!!
Keep building
Simon