To be sure, not even Ael's coup necessarily establishes that the Star Empire would suddenly start to make do with just a single Praetor. Duane follows the old Roman model where numerous Praetors vie for power, often through sponsoring outrageous military enterprises; all references to "the" Praetor might go with an unvoiced "Which one, you ask? Of course the one relevant to this particular crisis!".
On the same vein, the Praetor that MW Bonnano kills off in "Probe" is said to be "third in rank" although factually the most powerful man in the RSE. By the time of DS9 "Inter Arma", it may be that this de facto
arrangement has gained a de jure
basis, as Neral's position as Praetor is equated with "the top post". OTOH, there may of course be more than one "the top post", despite the definite article - and all the conspiratory talk between Ross and Bashir in that episode may be de facto
rather than de jure
Personally, I feel the RSE could have a male Praetor or eight even if Empress Ael remained in power. Then again, I wouldn't bet fortunes on anybody staying in power in the RSE for long.