If the question is whether to treat the 2 platforms as "2 different rdbms", the answer is a resounding "no".
The core product performs identically on both platforms with virtually no differences. Some add-on tools don't work on Windows, because of limitations of Windows.
- Case folding in database and table names -- easy to work around.
- File path use
\ -- whoopie.
- Symlinks -- does anyone care?
- Use of Galera, mysql sandbox, LVM snapshots, etc. These are tools for production environments; the big players do not even consider Windows when buying production servers.
I answer lots of forum questions. In the back of my mind, I think about whether the answer depends on version, SSD drives, OS, memory size, etc. Almost never is OS a factor in the answers.
Even the bytes on MySQL's files are identical.