R5 - If you don't keep this rule, you cac get an increase in subthreshold current, because high stress of STI on the AA effects mobility of AA.
Another problem, especially in short channel transistors, is a lower L effective, due to optical problems in the manufacturing - the drawn rectangle of the poly will actually be round, and if the extension of the poly beyond AA is not long enough, you will have a shorter L in the poly that is near the AA edge.
R-17: If the enclosure of the AA around the contact is not big enough, the contact resistance will increase due to stress of the AA edge on the contact