A fillet weld is deposited on the joint, whereas the groove weld is deposited in the joint (my definitions). The fillet weld is only required to have fusion to the root.
I would reference figure 5.4 taken from AWS D1.1: 2008 (or earlier). The sketches in the figure show fusion to the root except in the case where there is incomplete fusion to the root where it is consider to be a defect. Whereas there are no dimensions listed for the degree of incomplete fusion at the root, I take the position that any incomplete fusion at the root is unacceptable.
I would also direct your attention to the visual acceptance criteria provided by D1.1: 2008 (clause 4.8.1.2) for procedure qualification and welder performance qualification for fillet welds. The visual acceptance criteria and the macroetch test results for the fillet break test require fusion to the root, but not necessarily beyond the root.
By the very nature of a fillet weld, wherein the weld is deposited on the joint, complete joint penetration is not required. Where that the case, that is, were joint penetration required, the weld would be classified as a groove weld and the weld size would determine the depth of joint penetration required. As it is, the size of the fillet weld is determined by the leg of the fillet weld if it is flush or if it is convex. If the fillet weld is concave, the size is determined by the leg dimension of the largest inscribed isosceles right triangle. The definition of the fillet weld leg is included in A3.0 “Standard Welding Terms and Definitions”, likewise the definition of the fillet weld size is provided. Figures B25 A, B, and E included in AWS A3.0 leaves little wiggle room to argue the meaning of the length of the fillet leg by depicting the leg as extending from the joint root to the toe of the fillet weld.
Joint penetration is not a defect, but penetration beyond the root is not a requirement of a fillet weld based on the definition of the fillet weld size per AWS A3.0. AWS D1.1 references A3.0, so there is a basis to use the definitions provided by A3.0 as long as the glossary containing in the Annex of D1.1, does not address the issue.
Best regards - Al