This is probably too niche for anyone to spend much time on, but:
I do lots of readaloud (media-overlay) epubs, and sometimes have to manually create a new .smil file so one of the XHTML files can have synchronized word highlighting.
Currently I unzip the epub, duplicate one of the .smils, rename it XYZ, rezip the epub, manually add the XYZ filename to the manifest, associate it with the appropriate XHTML file in the opf, use one of the existing <par>s from the original .smil as templates to create new ones, add ids to the appropriate word spans to the XHTML to match what the <par>s are calling for in the XYZ .smil, and probably a few things I'm forgetting.
This takes ten minutes or something, so it's not like it's fatal, but can some part of this process be automated? Maybe something like select "Add blank SMIL file," then the dialogue is something like: "Ask me what XHTML this should be associated with, then give me a generic <par> line that has that XHTML in it with a generic fragment identifier," it gets added to the opf in the right ways, and then I can take it manually from there?