Sometimes, it's easier to see what happens if you use that conditional
formatting in a helper column of cells.
I added another column and plopped this into E2 (for me)
=MOD(SUBTOTAL(3,$A$2:$A2),2)
Then I dragged down to match the number of rows in the data.
You'll notice that when nothing is filtered, you get:
1,0,1,0,1,0,1.... (alternating 1's/0's)
Now filter that list:
The visible cells in that helper column still look like an alternating sequence
of 1,0,1,0,...
The =subtotal() function respects hidden cells (when hidden by an autofilter).
And =subtotal(3,$a$2:$a2)
counts (the 3 portion)
the number of cells that have something in them from A2 to the row you're in.
Note that if you used a column that somes contained empty cells (not formulas
that evaluated to ""), then you're formula will not work the way you want.