For reference, I am using Builder 3.36. My assumption based on your post is you're looking only for your application binary, and not a way to build some other package like .deb or .rpm.
There are a few ways you can do this.
Method 1: From your Flatpak build's directory
Click the omnibar and click "build", not "Export Bundle". When it's completed, click the "View build console contents" button from the same omnibar drop down where the "Export Bundle" button is.
Look at the last lines of output in the terminal for the "flatpak build" command. Look for the "build-dir" parameter passed to this command.
The path will be something like "~/.cache/gnome-builder/projects/AppName/builds/org.your.App.json-flatpak-org.gnome.Platform-x86_64-3.34-unversioned"
Go into this directory. It will have a subdirectory "src" which has your app.
Method 2: Change build configuration
If you click the "Switch Surface" button in the top left and go to "Build Configurations" you should see two configurations created for you by default (if you created the project through Builder). Builder defaults to your JSON file which builds Flatpaks.
Click the "Default" configuration, then click "Make Active" under "Overview". Then you can build the app as normal (e.g. with the omnibar at the top). Once it says "Build succeeded" the binary has been built.
But where? Look for the path listed in the "Overview" for the "Default" configuration -- under "Install Prefix". This will be something like "/home/user/.cache/gnome-builder/install/AppName/host"
In there is a "bin" directory with your app.
Method 3 (Preferred): Build using ninja
From the Editor surface, press CTRL+SHIFT+ALT+T to open a terminal inside Builder, which defaults to your $BUILDDIR
In the terminal that's open, simply type "ninja". If it says "ninja: no work to do." your app is already built and up to date. You can type "ninja clean" and then "ninja" if you want to do a fresh rebuild.
Inside this directory, (something like "~/.cache/gnome-builder/projects/AppName/builds/default-host-unversioned") there will be a "src" directory which is where the app is built.
Running your app
You may not be able to double click this from a file manager, so open the directory in a terminal and type "./appname" to run the app.