Fix: respect write_empty_chunks when opening an existing array

[ianhi]

When you opened an existing array the write_empty_chunks config was being ignored. As indirectly reported in pydata/xarray#10633 this fixes the one branch of this function where the config was not being handled

minimal zarr reproducer

#!/usr/bin/env -S uv run
# /// script
# requires-python = ">=3.10"
# dependencies = [
#     "zarr@git+https://github.com/zarr-developers/zarr-python.git@main",
#     "numpy",
# ]
# ///

import os

import numpy as np
import zarr

# Create array
store = zarr.open_group("test.zarr", mode="w")
arr = store.create(
    "data",
    shape=(20,),
    chunks=(10,),
    dtype="f8",
    fill_value=0.0,
    config={"write_empty_chunks": True},
)

# Reopen (like xarray does with regions)
store = zarr.open_group("test.zarr", mode="r+")
arr = zarr.open(store=store.store, path="data", config={"write_empty_chunks": True})

# Write zeros - should create chunk but doesn't
arr[0:10] = np.zeros(10)

# Check what was written
chunk_dir = "test.zarr/data/c"
chunks = (
    [f for f in os.listdir(chunk_dir) if f.isdigit()]
    if os.path.exists(chunk_dir)
    else []
)
print(f"Chunks written: {sorted(chunks)}")
print("Expected: ['0'] (chunk with zeros should be written)")

• Add unit tests and/or doctests in docstrings
• [NA] Add docstrings and API docs for any new/modified user-facing classes and functions
• [NA] New/modified features documented in docs/user-guide/*.rst
• Changes documented as a new file in changes/
• GitHub Actions have all passed
• Test coverage is 100% (Codecov passes)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.55%. Comparing base (2271067) to head (df48627).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3378   +/-   ##
=======================================
  Coverage   94.55%   94.55%           
=======================================
  Files          79       79           
  Lines        9448     9448           
=======================================
  Hits         8934     8934           
  Misses        514      514           

Files with missing lines	Coverage Δ
src/zarr/api/asynchronous.py	87.62% <100.00%> (ø)

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