This supposed loophole to 'abuse' of Article 3 is closed by Article 4, Chapter 1, Section 4 requiring there be more than one sponsor to a bill against fellow members which resolution 1488 was

Each and All members of the Alpha Nations shall have the right to introduce and sponsor resolutions except: […] 4. it's unilaterially introduced and entails action against a member state, in which case it shall be required co-sponsors for it to come to a vote

As for Ex post facto, this is implied, even if it was explicit, Alpha would still not be effected by it due to the fact he is God

“if a simple majority of people are absent any law can be passed even if all present vote agaisnt it ”

Good point, this clause was written as motivation for members to actually attend votes with it's intention to keep them from bitching about missing votes on resolutions they did not wish passed, with the members being marked as 'absent' on the voting rolls regardless

for Article 5, this was only to be used in response to Article 9 events or major events between voting sessions such as your coup of the AN

To Article 9, for a NWO conspiracy theorist like your self, if you actually read closely it you should have noticed something else… “resolutions passed by the AN shall [now] be applicable to that state including sanctioning of military action outside of the rules of engagement and legal dissolving of that state with a resolution ”, no where does it state this same action can not be applied to member states with Article 4, Chapter 1, Section 4 even giving the legal means to introduce such a resolution, but of course, even then there's safeguards considering a single Veto instantly kills the bill