Welcome to micromanaging hell
The term micromanaging doesn't fit here. You build up a factory/warehouse once and then it runs automatically. No micromanagement needed. If you don't even want to design the building you can just build a predefined warehouse/factory.
How does loading work when trains are longer than the warehouse? Will they move so all wagons eventually are loaded, or will they simply be loaded slower, similar to OTTD, or maybe not load additional wagons at all...?
Not finally decided yet. But if there are ramps for unloading the wagons, they represent the only position where a loading/unloading process takes place. Thus the answer to your question is: No, additional wagons wont be loaded at all.
I think there could be two possible options for "too long trains":
A) The train moves after having loaded the wagons which are currently positioned near the ramps so that other wagons can be loaded. Advantage: No shunting locomotives required.
B) A big train is split into smaller wagon groups which are moved by shunting locomotives. Advantage: You can serve multiple load ramp zones at the same time. Disadvantage: Shunting takes some time.