ファイル権限が許可されている操作と一致しません...？

CentOS 9 VMのファイル権限に関するいくつかの問題が発生しました。私は以前これほど多くの問題を経験したことがなく、インストール中に選択したセキュリティオプションとファイルシステム（GUI STIGとext4）に関連しているかどうか疑問に思います。

質問例1：

同じディレクトリにある2つのPythonファイル、lsとstatは同じ権限を表示します。

$ls -al config.py run_app.py
-rwx------. 1 myuser myuser 20K Aug  4 19:33 config.py
-rwx------. 1 myuser myuser 50K Jul  8 10:51 run_app.py

$stat config.py run_app.py
  File: config.py
  Size: 19873           Blocks: 40         IO Block: 4096   regular file
Device: fd05h/64773d    Inode: 1971283     Links: 1
Access: (0700/-rwx------)  Uid: ( 1000/myuser)   Gid: ( 1000/myuser)
Context: unconfined_u:object_r:user_home_t:s0
  File: run_app.py
  Size: 51016           Blocks: 104        IO Block: 4096   regular file
Device: fd05h/64773d    Inode: 1969096     Links: 1
Access: (0700/-rwx------)  Uid: ( 1000/myuser)   Gid: ( 1000/myuser)
Context: unconfined_u:object_r:user_home_t:s0

しかし、lsattrは正しく機能しません。

$lsattr config.py run_app.py
--------------e------- config.py
lsattr: Operation not permitted While reading flags on run_app.py
$sudo lsattr run_app.py
--------------e------- run_app.py

run_app.pyをcat/編集/実行することもできません。これらの3つのタスクはconfig.pyでうまく動作しますが。 run_app.pyを使用するすべてのタスクにはSudo / rootが必要です。

質問2の例：

Pythonパッケージは仮想環境にはインストールできませんが、ローカルユーザー環境にはインストールできます。

myuser@COS9-VM:~/sandbox
$python3 -m venv myvenv

myuser@COS9-VM:~/sandbox
$. myvenv/bin/activate

(myvenv) myuser@COS9-VM:~/sandbox
$python3 -m pip install pyyaml
Traceback (most recent call last):
  File "/usr/lib64/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib64/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/__main__.py", line 29, in <module>
    from pip._internal.cli.main import main as _main
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_internal/cli/main.py", line 9, in <module>
    from pip._internal.cli.autocompletion import autocomplete
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_internal/cli/autocompletion.py", line 10, in <module>
    from pip._internal.cli.main_parser import create_main_parser
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_internal/cli/main_parser.py", line 8, in <module>
    from pip._internal.cli import cmdoptions
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_internal/cli/cmdoptions.py", line 23, in <module>
    from pip._internal.cli.parser import ConfigOptionParser
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_internal/cli/parser.py", line 12, in <module>
    from pip._internal.configuration import Configuration, ConfigurationError
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_internal/configuration.py", line 21, in <module>
    from pip._internal.exceptions import (
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_internal/exceptions.py", line 7, in <module>
    from pip._vendor.pkg_resources import Distribution
  File "/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_vendor/pkg_resources/__init__.py", line 80, in <module>
    from pip._vendor import appdirs
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 846, in exec_module
  File "<frozen importlib._bootstrap_external>", line 982, in get_code
  File "<frozen importlib._bootstrap_external>", line 1039, in get_data
PermissionError: [Errno 1] Operation not permitted: '/home/myuser/sandbox/myvenv/lib64/python3.9/site-packages/pip/_vendor/appdirs.py'

(myvenv) myuser@COS9-VM:~/sandbox
$deactivate

myuser@COS9-VM:~/sandbox
$python3 -m pip install pyyaml
Defaulting to user installation because normal site-packages is not writeable
Collecting pyyaml
  Using cached PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (661 kB)
Installing collected packages: pyyaml
  WARNING: Value for scheme.platlib does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
  distutils: /home/myuser/.local/lib/python3.9/site-packages
  sysconfig: /home/myuser/.local/lib64/python3.9/site-packages
  WARNING: Additional context:
  user = True
  home = None
  root = None
  prefix = None
Successfully installed pyyaml-6.0

アイデアが足りません...私は何を見逃していますか？