1. is there a way to set default preferences that will ALWAYS apply, even to new Galleries and unless explicitly overridden.
Unfortunately not. There is no way to automatically have Juicebox-Pro use IPTC metadata for image title or captions as soon as the application has loaded.
You would always need to select 'Images -> Titles -> Use IPTC Title' (or 'Images -> Captions -> Use IPTC Caption') from the drop down menu at the top.
Since Juicebox has not created files with captions metadata we can't just reread the files after changing that option.
If you were to edit a gallery (via the 'Open Gallery...' button on JuiceboxBuilder-Pro's 'Start' tab) and the source images are still in their original '/export/galleryname1' folder from when the gallery was first created, then JuiceboxBuilder-Pro will reuse the source images (with the embedded metadata) instead of using the gallery images (without the metadata). (This is what the sourcePath entries in a gallery's XML configuration file are for.)
As long as the source images are still in their original folder, you could edit a gallery and quickly select 'Use IPTC Title' or ('Use IPTC Caption') before resaving the gallery on the 'Publish' tab.
I'm not sure if this will be helpful to you or not but I thought I should mention it.
And 2. which is not so much a question as a request for confirmation. The files created for the juicebox images directory, if captions are off in presets, don't include metadata.
That is correct. Images that are processed for a gallery by JuiceboxBuilder-Pro (either for resizing or watermarking) do not contain any metadata. The only way to avoid this would be to deselect the 'Resize Images' and 'Use Watermark' checkboxes. In doing so, JuiceboxBuilder-Pro will copy the source images across to the output 'images' folder without processing them (with their metadata intact).
In other words, the refresh that you mentioned in your 2016-06-24 response only works if Juicebox has copied over the image files with caption metadata and as far as I can tell it doesn't do that if captions are "off".
Please see my note above regarding the sourcePath entries (and editing a gallery with JuiceboxBuilder-Pro reusing original source images containing metadata). Leaving your source images in their original locations means that they can be reused (and their metadata can be extracted) when a gallery is edited.
It would also be helpful if you could shift-click or ctrl-click the list of images in a Gallery in order to delete them.
You can. You can Shift-Click and/or Ctrl+Click images on JuicboxBuilder-Pro's 'Images' tab and then go to 'Images -> Delete' from the drop down menu at the top (or press Ctrl+D). If you find that you can't do this, make sure that you are using the latest version of JuiceboxBuilder-Pro (v1.5.0). If necessary, instructions for upgrading Juicebox can be found here.
Thank you for posting your suggestions in the Feature Requests thread.
I do not know the likelihood of any suggestions being implemented but this is certainly the best place to post your ideas.
Edit:
Please also see my reply to your post in the Feature Requests thread here.