Core state factories vs occupied/annexed state factories. Total factories will be lower for you as the occupying power in that same piece of ground; i.e. Lithuania could have X factories as Lithuania on Lithuania's cores. Poland, on non-core area in Lithuania, will not have as many slots available.
Correct. Non core max slots is half of the max you get when it is a core. This excludes the extra slots awarded through NF's. Any excess slots are removed at the peace conference when you annex.
This is a rule that predates the changes made by La Resistance, where after annexing you got full use, instantly, of all the factories in the annexed states. Since occupation in the old system gave you (on average) 50% usage of the existing factories, this rule was there to give you roughly the same number of usable factories before and after annexation.
La Resistance has changed the rules, though. Even in annexed non core states you still have to deal with resistance and compliance. Which reduces the usage of the existing factories by the level of compliance. Cutting the 50% from the annexation (which actually removes slots and factories) by another percentage.
It is therefore better to make the states into puppets instead of annexing them outright. If you feel that the current system is too harsh though, you could always make a suggestion in the suggestions forum to have it looked at.