I noticed something similar as well.
I explain this to myself with (among other reasons) the ability to recruit mercenaries.
Medium - no mercenary recruitment, therefore an advantage for large empires with not that many foes around so that they can concentrate their large armies - which they have thanks to their higher "units/turn capability" (

) - on the few fronts they have to worry about, while small factions and factions surrounded by several enemies are at a serious disadvantage.
Hard/Very Hard: The smaller factions can compensate their lack of provinces to draw units from by hiring mercenaries, the money script often working in their favour as well since the AI seems to spend the additional money on buildings as well. And it's a difference if you have 1 settlement to build in or 20+ ...
And the Seleucids in particular seem to be pestered by rebels on H/VH difficulty, to a much higher degree than other factions. Which is of course not helping their economy....
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