Tectonic does not handle everything yet, unfortunately. I am guessing the same holds for your glossary and acronyms. So, same holds as with biber: how do you build the glossary and acronyms locally? (I’m not going to dig through your thesis to find that out). Then do the same on Travis.
If you believe Tectonic should support this, check for issues at https://github.com/tectonic-typesetting/tectonic/issues or create one yourself (including sufficient information about how you are building your glossary/acronyms).