Merge or Join Clips?

Nested clips is the only way. 
Given clip metadata is different from clip to clip, and ScreenFlow may need that metadata, there's no way to merge different clips. If you need to handle multiple clips as one, that would require a transcode which you should do before importing into ScreenFlow.

If you split a clip in ScreenFlow, the full clip is always available. Depending on what you're trying to do in the timeline, you can delete one portion and then stretch out the remaining portion.