[Python] `flatc --python` silently overwrites existing `__init__.py` files

**flatc version:** 25.12.19 (also older)
**Generator:** `--python`

## What

`flatc --python` creates an empty `__init__.py` in every folder of the
namespace path. If one of those folders already has a hand-written
`__init__.py` with code in it, flatc replaces it with an empty file without warning.

## Why

I wanted the generated files to live under my apps ipc folder which deals with the websocket server and the flatbuffer stuff

## Repro

Project already has these real files:

```
src/myapp/__init__.py # e.g. `def main(): ...`
src/myapp/ipc/__init__.py # e.g. re-exports
```

`schema/foo.fbs`:

```fbs
namespace myapp.ipc.generated;
table Thing { x: int; }
```

Run:

```
flatc --python -o src schema/foo.fbs
```

Now `src/myapp/__init__.py` and `src/myapp/ipc/__init__.py` are empty.
I found it happened through basedpyright lsp:
`ImportError: cannot import name 'main' from 'myapp'`.

## Expected

flatc should not destroy source files it did not generate. Any of:

- don't touch an `__init__.py` in a folder that already exists
- never overwrite a non-empty `__init__.py`
- only write `__init__.py` for the innermost namespace folder
- add a flag like `--python-no-init`

## Notes

- `--gen-onefile` skips the `__init__.py` chain but doesn't emit
cross-schema imports, so it breaks for schemas that use `include`. Not a
workaround.
- `--ts` is fine — it writes into a fresh tree and doesn't clobber
hand-written files.
- `flatc --help` (25.12.19) has no flag to control `__init__.py` output.

## Workarounds

1. Generate into a temp dir, move only the leaf namespace folder into place.
2. Give the generated code its own top-level package, with a namespace
prefix no hand-written module shares.

Start with the flatc --python entry point and reproduce the issue using schema/foo.fbs and the command shown. Trace how the namespace __init__.py files are written, then add coverage showing existing non-empty files are preserved and run the relevant flatc tests.

Written by the indexing model from the issue text.