The version of Junicode hosted here is no longer being updated. I'll be glad to include these new characters in Junicode 2, hosted on GitHub.
Bold and Bold Italic have always had fewer glyphs. One of the goals of Junicode v. 2, being developed at Github, is that all faces should have the same set of glyphs. Look for a release sometime in 2022.
The line spacing settings in the font were revised (somewhere along the line) to conform with current best practices. The difference in your case probably comes from the typoLineGap setting, which was 512 and is now 900. You can download version 0.7.6 from this site: if it was serving your needs before, there's no reason not to use it now. Or you can grab the current version, 1.002, at https://github.com/psb1558/Junicode-New/tree/master/legacy and use a tool like ttx to change the line spacing yourself....
There is a major revision to Junicode underway at https://github.com/psb1558/Junicode-New, and most new features will be included in that version rather than the version hosted here. The new version is not ready for prime time, but I have added a "legacy" folder there, where I will leave bug fixes and minor enhancments to Junicode (especially to the bold and bold italic faces, which because of their relatively small size are easier to work with than regular and italic. The changes to bold italic...
I don't know how I missed this issue when it first came up. Your diagnosis is right, though there are further complications having to do with Unicode normalization. All this will be fixed in the major remake of Junicode currently underway at https://github.com/psb1558/Junicode-New, under the name JuniusX.
I will include this in the new version of Junicode (currently called JuniusX) at https://github.com/psb1558/Junicode-New. I will include a few changes the legacy version of Junicode hosted here, but this version is not actively under development.
I'll add this, though adding things to Junicode is not so easy just now. It will at least appear in the remade version currently under development: https://github.com/psb1558/Junicode-New
It never occurred to me to provide this feature, but it makes sense. I'll look into it.