Can you configure Batch Capture settings to include padding on both in and out points? For example configure to capture 3 additional seconds on each end?
Not that I'm aware of.
The simple solution is to subtract & add 3 sec. from your in and out points.
This assumes that you have enough material to do this.
If you're like me who shoots at least 5-10 sec. of a scene before and after anything critical (long time habit that works quite well), this isn't an issue.