So it's an unlikely scenario, but: I've stacked three tractor tokens on an agility 2 ship. I then shoot at it at range 3 (or through a rock). Will it still roll one defence die as that's a bonus die rather than an agility increase? Thanks

Correct. Range 3 and / or obstruction dice are bonus dice that have nothing to do with a ships agility at all.

EDIT: which is one of the reasons why Expose works so well on a Decimator.

Only way to cancel range bonus is to use secondary weapons.

Only way to cancel range bonus is to use secondary weapons.

Or be Zertik Strom.

Only way to cancel range bonus is to use secondary weapons.

Or be Zertik Strom.

Or be the Inquisitor

So it's an unlikely scenario, but: I've stacked three tractor tokens on an agility 2 ship. I then shoot at it at range 3 (or through a rock). Will it still roll one defence die as that's a bonus die rather than an agility increase? Thanks

Ship agility always ends up at a minimum of 0 no matter how many points get taken away from it. Then you add dice for range and obstacles after you have calculated how many you get for agility so it would be possible for the ship to still roll 2 die after you hit it with 3 tractor tokens if it is at range 3 and you are obstructed.

Correct. Range 3 and / or obstruction dice are bonus dice that have nothing to do with a ships agility at all.

EDIT: which is one of the reasons why Expose works so well on a Decimator.

If only there were two EPTs slots on the Decimator.

Oicunn + Isard + Expose + Experimental Interface = tears. Especially if you were cool enough to grab a TL the turn before smashing into the target. Add in Vader for extra nerdrage. Leave gunner out of it.

Edit - but to "stay on target", you start with the dice from agility after all penalties. Then add dice from bonuses, such as range and obstructions. Then roll the dice. During modification, add dice/tokens from other effects.