hell if I know, give it a shot and see what happens.
Basically, the only thing it does is tell EVE to 'warp me to stargate' rather than the autopilot's version that takes you to within 15km. So, it'd be no different than using the right click menu and warpning to a stargate. If a "bubble" hits you while doing that, then it'd do the same thing while using this feature.