[Bug]: manifests using autoconf sometimes fail to find a usable shell inside nspawn container

[H-Sachse]

Checklist

• I agree to follow the Code of Conduct that this project adheres to.
• I have searched the issue tracker for a bug that matches the one I want to file, without success.

flatpak-builder version

1.0.12

Flatpak version

1.14.1

How to reproduce

From inside an nspawn container

1. git clone --recurse-submodules https://github.com/flathub/org.openttd.OpenTTD.git
2. cd org.openttd.OpenTTD.git
3. flatpak-builder --disable-rofiles-fuse --force-clean build-dir org.openttd.OpenTTD.yaml

Expected Behavior

builds cleanly

Actual Behavior

[snip]

Building module SDL2 in /home/hesa/devel/flatpak/org.openttd.OpenTTD/.flatpak-builder/build/SDL2-1
========================================================================
./configure: This script requires a shell more modern than all
./configure: the shells that I found on your system.
./configure: Please tell [email protected] about your system,
./configure: including any error possibly output before this
./configure: message. Then install a modern shell, or manually run
./configure: the script under such a shell if you do have one.

Additional Information

Environment:
Host is a debian buster with debian bullseye in an nspawn container.
flatpak and flatpak-builder are from bullseye-backports, but show same behaviour as the bullseye proper versions.
Running ./configure and make from the failing directory works without issue so I have no idea why the shell detection fails for flatpak-builder.