Generally speaking, the default Questing Botbase is linear, it perform scripted behaviors one-at-a-time, so for compatibility it is not recommended to use Plugins, aimed at heavy movement (like chest collecting ones) with complex questing profiles (like Kicks 1-100 for example) for several reasons.
1. The plugin itself, (unless it is part of the questing profile, Like Thebrodieman's, which plugins work in synergy with his questing profiles) is completely unaware what the Questing profile is performing, and it could interrupt a critical behavior, coded within the Quest profile - like Escort, gauntlet or scripted "dance" behavior.
I think this is the sole reason, why Questing is not recommended to be run in Mixed mode too.
2 With the above taking into account, if plugin is being developed, obviously it cannot timelapse to former moments of time, but a good move would be to pause the plugin, when incompatible behavior is performed by the botbase. I can see this only if the profile and plugin work in synergy. Both should be aware of the "other's presence"