DataFrame arithmetic functions with multiindex, NaN index values, and fill_value set returns an invalid result with non-unique index.
#### Code Sample, a copy-pastable example if possible

```python
from unittest import TestCase

import numpy as np
import pandas as pd


class TestSubtract(TestCase):
    def test_subtract_partially_aligned_multi_index_dataframes_with_nans(self):
        df0 = pd.DataFrame(
            data=[
                [1, 2],
                [3, 4],
                [5, 6],
                [7, 8],
                [9, 10],
                [11, 12],
                [13, 14],
                [15, 16],
                [17, 18],
            ],
            columns=["happy", "sad"],
            index=pd.MultiIndex.from_product(
                [["a", "b", None], [0, 1, np.nan]], names=["l0", "l1"]
            ),
        )
        df1 = pd.DataFrame(
            data=[
                [1, 2],
                [3, 4],
                [5, 6],
                [7, 8],
                [9, 10],
                [11, 12],
                [13, 14],
                [15, 16],
                [17, 18],
            ],
            columns=["happy", "sad"],
            index=pd.MultiIndex.from_product(
                [["b", "c", None], [1, 2, np.nan]], names=["l0", "l1"]
            ),
        )

        result = df0.subtract(df1, fill_value=0)
        expected = pd.DataFrame.from_records(
            [
                ["a", 0, 1 - 0, 2 - 0],
                ["a", 1, 3 - 0, 4 - 0],
                ["a", np.nan, 5 - 0, 6 - 0],
                ["b", 0, 7 - 0, 8 - 0],
                ["b", 1, 9 - 1, 10 - 2],
                ["b", 2, 0 - 3, 0 - 4],
                ["b", np.nan, 11 - 5, 12 - 6],
                ["c", 1, 0 - 7, 0 - 8],
                ["c", 2, 0 - 9, 0 - 10],
                ["c", np.nan, 0 - 11, 0 - 12],
                [np.nan, 0, 13 - 0, 14 - 12],
                [np.nan, 1, 15 - 13, 16 - 14],
                [np.nan, 2, 0 - 15, 0 - 16],
                [np.nan, np.nan, 17 - 17, 18 - 18],
            ],
            columns=["l0", "l1", "happy", "sad"],
        ).set_index(["l0", "l1"])

        print(expected)
        print(result)

        pd.testing.assert_frame_equal(expected, result)
        self.assertTrue(result.index.is_unique)
```
#### Problem description

I have two data frames with multi-level indices that represent the same sets of values, although both data frames may have index values that are not represented in the other (In my case, I am comparing two SQL queries results with a shifted date time index for week-over-week comparison). I'd expect the `DataFrame.subtract` function using fill values to replace a missing value on either side of the data equation with the fill value. Instead, I am seeing a value returned with a mismatched index with non-unique values.

In my expected dataframe in the test case, I populate each value with the expression I would expect the `subtract` function to perform.

#### Expected Output

#### Output of ``pd.show_versions()``

<details>

[paste the output of ``pd.show_versions()`` here below this line]
pd.show_versions()
INSTALLED VERSIONS
------------------
commit           : None
python           : 3.6.8.final.0
python-bits      : 64
OS               : Darwin
OS-release       : 18.7.0
machine          : x86_64
processor        : i386
byteorder        : little
LC_ALL           : en_US.UTF-8
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8
pandas           : 0.25.3
numpy            : 1.16.2
pytz             : 2019.1
dateutil         : 2.8.0
pip              : 18.1
setuptools       : 40.6.2
Cython           : None
pytest           : None
hypothesis       : None
sphinx           : 2.0.1
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : None
html5lib         : None
pymysql          : 0.8.0
psycopg2         : 2.7.3.2 (dt dec pq3 ext lo64)
jinja2           : 2.10.1
IPython          : 7.5.0
pandas_datareader: None
bs4              : None
bottleneck       : None
fastparquet      : None
gcsfs            : None
lxml.etree       : None
matplotlib       : 3.0.3
numexpr          : None
odfpy            : None
openpyxl         : None
pandas_gbq       : None
pyarrow          : None
pytables         : None
s3fs             : None
scipy            : None
sqlalchemy       : None
tables           : None
xarray           : None
xlrd             : None
xlwt             : None
xlsxwriter       : None

</details>
