Bonuses for factories?

Look at ..\Victoria 2\common\production_types.txt and you can see them all there. The game, for some reason, does not display them to the user, but basically, any factory that is placed in the same region as where the resources it needs are produced, will get a throughput bonus. If a factory needs grain, then having a state with grain as an RGO on any province in that state will boost throughput of the factory. If you have a factory that requires another manufactured good (like machine parts), then having a factory producing that good in the same state as the factory you're looking to build will give it a throughput bonus too. Most of the throughput bonuses are 10% (I think?). Some advanced factories will get 15% throughput bonuses, but those are only the factories that require other manufactured goods (i.e. an automobile factory).

Just as a reminder, factory throughput isn't output, but it can influence factory output. What it does is make each individual worker produce x% amount more, so it basically makes the workers work more efficiently, while also increasing the input requirements of the factory by x%.

Input and output bonuses are critical for countries with low prestige, as they will have difficulty getting stuff on the market and thus need to get the most from the least amount of raw materials.

If you hover over the input goods it shows the synergy bonus's in game. (If its not input goods just check the whole factory block, its there somewhere.)