You can define a new issue type (for auto-fire issues say Scheduled Job) and attach that new issue type to new workflow (which bypasses the approval checks). Then amend all scheduled issue creating jobs through your plugin to create scheduled jobs using the newly defined issue type.
This way all scheduled jobs will be created with new issue type which will be associated with a workflow that bypasses your additional approval checks.
Hope it helps.
Unfortunately TheScheduler doesn't allow to bypass some part of the workflow, but we see this as thing to be done in the future. Even if our plugin would have such option we must remember that omitting some part of the workflow may result in inconsistency. Some workflow transitions may have related screens with required fields which user should populate in order to complete transition. If we bypass such transitions then some values for fields may be missing.
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