I think that is answered best in reverse order:
Officially, both Commanders and Thargoids must wait for Thursday for anything to change:
- Thargoids cannot attack anything until Thursday, and indeed they can not attack that system again until Thursday plus four weeks.
- Humans do not gain access to the completed system until Thursday, during which ports remain abandoned and Fleet carriers may not arrive.
- If populated, the Recovery state also blocks Fleet carriers—again, something which only actually changes on Thursday.
- For the purpose of Titan vulnerability, nothing changes until Thursday.
Despite a
few minor changes occurring mid-week, for the most part everything still must await Thursday before actions in the previous week have any appreciable effect.
Convenience, and due to Frontier preferring Commanders not to waste any war activity upon systems which are complete¹. The mid-week changes for a complete system are:
- No hyperspace destabilisation when jumping to it.
- No Thargoid interdictions.
- No Frame Shift anomalies.
- No port attacks or conflict zones.
- Info panel victory message.
- Comms panel victory message.
- Spire progress no longer applies.
So you can jump safely through the system, and you are prevented² from trying to fight Thargoids in the system—but most of those are very minor compared to the full war, and have no direct war effect until Thursday! The biggest actual war effect is the Spire progress, which was much more recent and allowed us to clear M. Indra much more sensibly than planned prior to that.
1. As stated by Derin at Frontier during Frameshift Live #24.
2. Hyperspace summoning by jumping to a nearby Control system should still work, of course.