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Refugee camps obviously will grant their bonus population to the city of their zone, but what about other things?

-Autofactories: Will the Industrial Points always end up at the SHQ eventually?
-Science Bonuses: I assume these don't care what zone their in
-Power Hexes: Will the power be transferred to where it's needed?

ORIGINAL: HansLemurson

Refugee camps obviously will grant their bonus population to the city of their zone, but what about other things?

-Autofactories: Will the Industrial Points always end up at the SHQ eventually?
-Science Bonuses: I assume these don't care what zone their in
-Power Hexes: Will the power be transferred to where it's needed?

First, you need to understand the storage rules:
Zones try to keep storage of 1 turn of consumption (2 for food). This includes future production and consumption

The order for the SHQ Logistics System is:
- Zone Delivieries. Trying to top up the storage goals
- Unit Deliveries.
- some other stuff
- Zone Consumption, inlcuding building
- Zone production

Local production can help a little in filling stores for the next turn. If the consumption is still the same. But in the end, IP and Energy travel for free on the logistics network so it hardly maters.

Resources like industry or power will go into the zone inventory, and if the zone has a surplus, it will send it to the SHQ. You can check the Items tab in the bottom panel to see what a given zone is doing with them. You don't usually need to worry too much about these, as transferring industry or power (or water & fuel) doesn't consume logistics points (it just requires a logistics connection that has points on it in the first place).

But I won't lose anything if I transfer control over a Crashed Spacecraft or an AI Computer Core to a Zone that is not my Capital?

ORIGINAL: HansLemurson

But I won't lose anything if I transfer control over a Crashed Spacecraft or an AI Computer Core to a Zone that is not my Capital?

No.