I don't know how bottling plants got carbon dioxide in the old days, but the bottling plants around here get tank cars of liquid sugar (mostly corn syrup) and liquified CO2. Coke was (is?) manufactured as a sweet syrup and shipped to local bottlers and restaurants. My guess is that in the old days the syrup was in barrels loaded into box cars. I'd sure like to know how where they got the CO2. :-)
When I was a kid Coke always came in returnable bottles in wooden packs that held 24 bottles. So my guess is that you'd only need enough new bottles at the plant to replace broken and lost bottles.
Soft drinks were mostly a post-auto era phenom, so a lot of bottlers never had rail connections.