Implemented in the next patch.

I tested it and i wasn't able to reproduce the problem, i'll try again with your latest save.
Thanks for providing a detailed report.

Try to click on the bridge, roads and train tracks are controlled from that window.

Correct, it's in the current experimental version.

Fixed in the next patch.

Correct, this happens with long rails due to how the scan\construction timings differ. It's on my TODO list.
Not an error per se but an annoying premature warning.

Fixed in the next patch + station\dock modules input-output indicators.

Can confirm, building a module while the train is loading\unloading triggers the issue.