I've been looking into similar nuances between the MM and MD guis. Nothing is very consistent. Sometimes its 'up' aps, sometimes its 'up+down'. My MM and MDs are off too because of stale APs on the MM that aren't in the MD database.
Here in my case the MM top banner shows 1620 Aps. But on the cluster overview row it shows 1617 active. But then if I click on the '1617' it then shows me a table of 1625 APs in the table but the large orange banner shows 1662 (shown below).
So I'm seeing 1620, 1617, 1662, 1625... are you kidding!? :)
They all means something different and its confusing. Now, 1620 (up) + 42 (down) = 1662 (total) so that sort of makes sense. But were is 1625 coming from.
Look at the actual MD guis and those numbers, and compare to the MM, try to add things up to make it make sense - cant be done easily.
Not really an answer to your question, but just agreeing I see many nuances and variations myself - and to me that's frustrating.