By the way, I know ttfautohint is for web typography but I guess I didn't realize until now that has nothing to do with the font embedding in PDFs, which should look fine. So what can I do to improve the appearance of my fonts in digital applications offline?

ttfautohint only adds truetype hinting, emulating the autohint used in FreeType. However TrueType hints are (for the most part) only used on windows systems, so they don't effect the way that PDFs are rendered.

However to answer your second questions about what to do for improvement, I think we'll need some more images to see exactly what the issue(s) are.

Using ttfautohint will also affect rendering in PDFs, at least when you view them with Adobe Reader or Acrobat.

But that only applies to ttf fonts then, right? Can I achieve greater results with a ttf than otf when it comes to PDF embedding?

I just created a PDF and you can see there are some slight rendering issues where some characters are a tiny bit thicker:

It's more obvious in Illustrator. Here's a screenshot:

The /i for example has more weight than /l even though they're the exact same on the bottom part. In print the problem disappears so it really seems to be a rendering issue. What can I do to improve things?

Hinting, whether of TrueType or PostScript outlines, affects most non-Apple rendering environments, including those from Microsoft, Adobe, and often FreeType*.

With “Adobe” you can include the rendering in Adobe Reader, Acrobat, InDesign, Photoshop and Illustrator—even on Mac OS.

* FreeType can be set to ignore hints in the fonts like Apple does, autohinting on the fly. Indeed, the TTFautohint hinting is based on the autohinting created for FreeType. But I gather many FreeType-based environments choose to respect the hinting in the font.

I meant that Adobe uses it’s own rendering engine for text in most of their apps, across platforms. Adobe’s rendering bypasses the OS rendering engine.