BUG: MultiIndex.equals returning incorrectly True when Indexes contains NaN
- [x] xref #38439
- [x] tests added / passed
- [x] passes `black pandas`
- [x] passes `git diff upstream/master -u -- "*.py" | flake8 --diff`
- [x] whatsnew entry

Depending on the expected behavior of align, this may have hidden an additional bug in align in the referenced issue.