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a6 is intended to point to $dff002 (DMACONR).
The code in question wants to read from $dff00a (JOY0DAT) which contains the current mouse cursor position.
... and setting a6 to $dff002 instead of $dff000 is a micro-optimization: there are probably a couple of places in your program where you want to access $dff002 but none where you want to access $dff000. Therefore your program will become a couple of bytes smaller by using $dff002 as your base pointer... although, as you already noticed, the sourcecode becomes a tad more confusing. Whether or not it's worth it is up to you.
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