bug: asdf-python intercepts mlx_lm.server installation and sets an old python version

### Provide environment information

```bash
I'm pretty confused by how asdf python works. I thought it was just working with python versions, but when I look at all the things in ~/.asdf basically every python command is there from nbdime or mlx_lm.server

I'm confused how I change these version. `asdf set python 3.12` In the new 0.16 does set it properly, but then nbdime then complains since it only has

asdf shimversion nbdime

python 3.12.7
python 3.11.8

So it gives the error

No version is set for command nbdime
Consider adding one of the following versions in your config file at /Users/rich/.asdf/shims/.tool-versions

Do I would have thought that an asdf reship with the python set to another would fix this, but the version seems to never change. How do you now reship these?
```

### To Reproduce

pip install nbdime
asdf shimversion nbdime

python 3.12.7
python 3.11.8

asdf set python 3.12.8
asdf reship

But

asdf shim versions nbdime

Doe snot change it looks like these shims just run "asdf exec nbdime"

### Describe the Bug

The reship does not use the latest version of python. So I'm not clear how I fix this, where is the directory of all the python executables controlled by asdf-python, that's probably where to start :-)

### Expected Behaviour

Well it would be nice to know how to reship with just a single python command. I've tried

asdf reship nbdime 3.12.8

but this doesn't work obviously

まず `pip install nbdime`、`asdf shimversion nbdime`、`asdf set python 3.12.8`、`asdf reship` を使って、報告された挙動を再現します。asdf-python による shim と選択された Python バージョンの処理を読み、その後、shim を再作成した後に `asdf shimversion nbdime` が選択されたバージョンを反映するか確認します。バージョンの挙動が修正されるか、サポートされている reship ワークフローが明確に確立されれば完了です。

索引モデルが issue の本文から書いたものです。