Investigating this a bit further, changing the shebang in
/usr/bin/ipython3 from "#!/usr/bin/python3" to "#!/usr/bin/env python"
solves the issue. But I guess this is in conflict with Debian's policy
on interpreter location, that says "/usr/bin/env name" should not be
used:
https://www.debian.org/doc/packaging-manuals/python-policy/ch-python.html#s-interpreter_loc
Replacing /usr/bin/ipython3 with Fedora's ipython3 initialization script:
#!/usr/bin/python3
# This script was automatically generated by setup.py
if __name__ == '__main__':
from IPython import start_ipython
start_ipython()
Fixes the issue, although I'm not certain what other consequences this has.