Mostly related with "Component Versions" feature of the add-on. Since some functionality of "Component Versions" overlaps with "Bundles" this section also contains some bundle related settings.

The settings that are 'Do not Allow Invalid Versions', 'Suffix to Append Invalid Versions', 'Highlight Invalid Versions', 'Append Bundle Name to Bundle Versions for Display', 'Allow All Versions for Unversioned Components', 'Applicable Versions in Multi-Component Issues', 'Always show bundle versions' can be overridden by project specific configurations.

Highlight Invalid VersionsOn issue page, plugin may highlight invalid versions. These invalid version may have been entered before the plugin is installed or the plugin may be configured to allow invalid versions.
Invalid Version Highlight ColorColor to use when highlighting invalid versions.
Append Bundle Name to Bundle Versions for DisplayIf bundle versions are shown on issue create/edit page, the plugin may add name of the bundle to name of the version. So that it is easier to select correct bundle if your bundle versions are not descriptive enough.
Allow All Versions for Unversioned ComponentsIf no version is defined for a component and only this component is selected, displayed versions depends on the value of this setting. If it is true, all project versions are displayed but if it is not checked no version is displayed.
Do not Allow Invalid VersionsIf it is true invalid versions are not displayed at all. If it is false, all versions are displayed but invalid versions are highlighted with a suffix and a color.
Suffix to Append Invalid VersionsOnly used if "Do not Allow Invalid Versions" is false. This suffix is added to all invalid versions in version selection fields.
Applicable Versions in Multi-Component Issues

Effective if multiple components are selected:

  • Intersection: Only the versions that are valid for all of the selected component are shown
  • Union: Any version that is valid even only one of the selected component are shown
Which Versions are Displayed When No Component Selected

Used when no component is selected:

  • All Versions in the Project: All versions defined for the project
  • Bundle Versions: Only the versions associated with a bundle are displayed.
Always show bundle versionsIf this option is checked, bundle versions are shown in addition to component specific versions when a component is selected.
Version Sort AlgorithmEffects in which order versions are listed.
Don't Show Archived VersionsIf selected hides archived versions from version lists.
Synchronize Component Versions with Project VersionIf this setting is turned on, component and project versions are synchronized if a project version is mapped to only one component version and not used as a version for any bundle. This is a two way synchronization for release status, release and start dates and description. If a project version is used more than one component  version or it is used as a bundle version, synchronization is not performed. 
Select Custom Version FieldsIf you are using custom version fields, any field selected here will behave like "Affect Versions", "Fix Versions" build-in fields and will be handle by the plugin.
Remove Version Groups FromBy default versions are grouped as "Released", "Unreleased". Depending on the setting here this grouping can be removed by the plugin.
Configuration Management RoleUsers in that role can configure subcomponents, create and configure bundles, create versions, create components and update component specific versions. They can also release component specific versions. Although they can remove component specific version they can't remove JIRA components and versions.
Allow Component Lead to Manage Component VersionsIf you enable this feature, component managers can create/update/delete component specific versions for their own components. They can't create new project components or versions or they can not manage component specific versions of other components (components that are lead by someone else). 

Remove Released Versions from 'Fix Version/s'' field

If selected, released versions are not shown within "Fix Version/s" field. But previously selected versions are not shown as invalid version.
Remove Un-Released Versions from 'Affects Version/s' fieldIf selected, un-released version are not shown within "Affects Version/s" field. But previously selected versions are not shown as invalid version.