the earliest army list of which I have got copies is the one of 1806.
In this, officers of the same name within the same regiment get a number are called the first, the second and so on, according to anciennity of rank. I believe, the numbering was within the same rank (all types of Capitains and all types of Lieutenats counting as one rank each).
Fähnriche are numbered together with Sekonde-Lieutenants (example: Graf zu Dohna, Dragoner-Regiment Auer - No. 6)
counter-example: Fähnriche are not numbered together with Sekonde-Lieutenants (example: v. Rappard, Infanterie-Regiment Tschammer- No. 27) (a different regimental tradition ? or, possibly more probable, a neglection by the publishers of the army list ?)
Majors are not numbered with Sekonde-Lieutenants (example: v. Winterfeldt, Infanterie-Regiment Treuenfels - No. 29)
Oberst-Lieutenants are not numbered with Stabs-Capitains (example: v. Puttkammer, Infanterie-Regiment Winning - No. 23)
I would say that officers lost their number if your name-fellow within the rank group was promoted or left the regiment. (in the former case in some cases the numbering would have probably been continued inofficially by the comrades, or the rank was added to make clear who was being talked of. But there were other ways of making differences, too: In the Landwehr battalion from the Pomeranian town Anklam, two officers, brothers and sons of a post master, were nicknamed "Extrapost" and "ordinaire Post")
Unfortunately, I couldn't find anything written about the Prussian system of numbering. If find some time, I will try to follow the of a "numbered" officer through the army lists for his regiment from 1806 to 1815, to verify my assumptions.
I don't have any information about the numbering of officers within the regimental lists for financial purposes - if there was any. But probablyit was similar to the Russian system (your number 1).
The listing of officers within their regiment in the army lists gives the highest ranks first, down to the lowest rank. Within each rank, those with higher anciennity are listed before those who did attain their rank later. Even though the officers do not get a number in the army lists, they knew their position very well, if a position of an officer became vacant, by right of anciennity it was filled by promotion of the highest ranking officer of the next lower grade. If an officer was promoted ahead of his more ancient comrades of the same rank, he was (always ?) transfered to another regiment, and if the highest ranking officer of a given rank was not to be promoted, vacancies above his rank had to be filled by officers from other regiments (Premier-Lieutenant v. Rahden of the 2. Schlesisches Infanterie-Regiment claims to have "blocked" promotions of Lieutenants his regiment in the 1820s or 30s, as the minister of war disliked him - I know there was a refutation of this claim printed after v. Rahdens memoirs were published, but I don't know its content).
In addition, in most Prussian regiments after 1808 you have the group of "aggregirte Offiziere" (your Russian "host" rank officers ?), who serve with the regiment but will not be promoted by the right of anciennity.