They probably use Javascript to hide/show the navigation bar as you scroll and my guess is that they set its position with Javascript instead of CSS.

I had bottom-bars appearing around 3/4 of the way down the screen on Firefox on my Android and never did find the actual cause (scoured about:config but no luck) but I solved it by clearing data and starting a new profile.

First I forced closed the app and backed up the file with my tabs using a file manager with root access:

/data/data/org.mozilla.firefox/files/mozilla_components_session_storage_gecko.json

Then cleared the data, launched it and signed in and such, forced it closed again, copied back the tab session file, and launched it again.

I just tried their site in fennec w/ NoScript and only have their main domain whitelisted. That bar appears at the bottom for me. Not sure what's going on here.