no matter what stat is used for agility while VR rigging/jumped in, the circumstance as described in the OP can be tricky simply because "cyberlimbs".
It'll inherently come down to GM's call when the task at hand involves just the cyberlimb(s) and when the task involves the entire drone's body, necessitating the averaging rules.
Averaging isn't well defined. The way chummer resolves it (and the way I also resolve it) there are six slots on the metahuman body, one for each potential cyberlimb (2 arms, 2 legs, 1 torso, 1 skull). That means there are 6 values considered for averaging. For example if you have an agi of 3 but one cyberarm with 9 agi, your "average" is 4 for tasks where the arm helps but the task isn't resolved by just using your arm.
Whether a drone can have cybertoros or cyberskulls is dubious, and the averaging may be dealing with 4 instead of 6 values when calculating the averaged effect of agility in a drone's cyberarm...
And of course since cyberlimb stat averaging is so ill-defined, a GM could potentially ignore the concept of a "static" number of slots and judge them on a case by case basis. Say you want to use a katana but you only have 1 augmented cyberarm. Instead of averaging against 6 (or 4) agility values perhaps the GM might say just average between the two arms, or the 2 arms plus core (torso). Or whatever.