Building this version of bubblewrap with Meson is recommended. The source release bubblewrap-0.9.0.tar.xz no longer contains Autotools-generated files, although this version can still be built using Autotools after running ./autogen.sh. Future versions are likely to remove the Autotools build system altogether.
https://github.com/containers/bubblewrap/releases/tag/v0.9.0
Consider switching to Meson. Not tested.