If PT says you have a .1 BB winrate with AT, you have that AFTER rake.

Think about it... when you put 2 bucks in a 5 dollar pot, and win 4.50 after the rake, you get a 4.50 pot. It is recorded as winning 2.50

So your numbers for AT would be like
+2.50
-1
-1

giving you .50 / 3 hands or about .18 a hand.

WITHOUT rake it would be
+3
-1
-1

So your win rate would be higher without the rake... but PT isn't fooling you into thinking you're winning with those hands, just not telling you why you're not winning MORE.

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-You may not know this, but poker is a game of incomplete information.