with Sisko it’s specifically because, until they discover the wormhole, DS9 is considered a backwater post.
Typically, base commanders are at least captain rank. Sometimes bases are commanded by lower ranks, and there can be different reasons but in this case: it’s remote and considered a less important “backwater” post compared to other bases. His eventual promotion to Captain belatedly corrects for how important the station became, as a trade/transit hub and as a strategic asset, after the wormhole discovery
Maybe I was a weird kid but I was keenly aware of the pips on the uniforms after the point in TNG where they vaguely explain how the rank insignia pips work. It was never for any particular reason except to know another “thing” about my favorite characters.
That’s not to say that you’re wrong, maybe that’s what they told themselves when they didn’t change it! But if so they definitely underestimated some fans, lol