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If you get a warning that the file cannot be saved, your ePUB has structural errors which needs to be solved first. Sigil does not allow saving structurally incorrect ePUB. That is a design choice and I think that is a very good one. You have the responsibility to make sure that the structure is correct, since you determine that via you XHTML. Sigil tries to help you with Tidy, but that is not always a good help.
Regarding using libraries... Back in the day cross platform compiling was not possible. You had to invent everything anew on each platform. Even the programs from 'back in the day' evolved into object oriented programming. It has faults, but more merits.
Again, font-handling is not complex but a precise job. The actual font included is not really important. So the fact that there are thousands of fonts is not relevant. The method remains more or less the same.
I think you need to read up on what ePUB exactly is and how it is structured. You keep referring to HTML, but in reality it is XHTML with CSS if you want. That is not the same, although very alike. Sigil can import HTML and convert it into XHTML, but expect some post-processing depending on the source.
A lot of people use the template idea. I also use it. I just have a small ePUB with only some basic xhtml files like the cover and titlepage and a default stylesheet. Not that it is required, but I don't want to import these every time. It saves a little time. Creating a template like that is easy. Open Sigil, import the files and save. If you get an error, read the error message and solve it.
If you just want to create an ePUB and don't really care about what is going on and how it looks, use another tool. If you want full control of your ePUB, use Sigil.
You can request as a feature an autosave of course. I know many programs that don't have an autosave feature and I don't miss it. I have a tendency to save on a regular base. After all, Ctrl+S is a very difficult keystroke to remember...
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