Android 10's gesture navigation does not yet support 3rd party launchers.

During the Android Q/10 beta process we saw Google rushing to bring their gesture implementation from a buggy mess to, well, a slightly less buggy mess. The biggest bug being that they don't work with 3rd party launchers. We've spoken to Google about this and in a blog post they acknowledge the issue and that they are working on a fix:

Custom launchers are another area where we’ve heard feedback and we’re continuing to work on issues, particularly with stability and Recents. Starting in Beta 6, we’ll switch users to 3-button navigation when they are using a custom launcher by default. We’ll address the remaining issues in a post-launch update allowing all users to switch to gestural navigation. Meanwhile, please continue to give us your feedback.

(The feedback link no longer accepts feedback)

"A post-launch update" means after 10.0, presumably 10.1 or 10.0.1 or 11.

Since then in an interview with 9to5google Dave Burke of Google "further confirmed that third-party launchers are working internally with gesture navigation".

Unfortunately there is nothing Nova Launcher can do right now to make this work. With the Android 10 source code drop we've verified that it's not something we can change from our end. The function isGestureNavSupportedByDefaultLauncher literally just checks if the launcher is a system app or not.