`api_version` set in `custom.py` is ignored

### Godot version

v4.8.dev.custom_build [457470a8d]

### godot-cpp version

d7b6162249ed52796a8301d216c24ee71d68c2bf

### System information

Linux

### Issue description

Error when trying to use `custom.py` to add the `api_version` instead of specifying it by CLI

### Steps to reproduce

Use `api_version` in `custom.py`

### Minimal reproduction project

N/A