When I put a station from blueprint with station combinator that has "Automatic allow-list" toggle disabled and with only 1 warehouse, and then add more warehouses via my modular per-wagon blueprint, only the first of all Cybernetic Combinators that are set to "Wagon control" mode outputs signals and sets filters on item slots in wagon when the multi-wagon train arrives.

To fix that for given station, I have to go into the station combinator, enable "Automatic allow-list", press "Refresh allow-list" and then disable "Automatic allow-list" again. Afterwards, when the next train arrives (even one that was already on route and was waiting for the "bugged" train to leave), all per-wagon Cybernetic Combinators (which are in "Wagon control" mode) correctly output signals and set filters.

So it has something to do with "allow-list" affecting the station even when "Automatic allow-list" is disabled.

https://i.imgur.com/cKgQGgq.png

On the screenshot, train expects 1000 of rare steel plates, but only the first wagon requested 500 of them via "Wagon control" combinator. The second combinator just does not work.