Well, you can create one more folder inside vault and create md files there.
Like:
Vault:
— .obsidian*
— notes
---- \note1.md
---- \note2.md
You can also try to set symbolic link for .obsidian folder, but I wouldn’t suggest this decision, if you don’t know exactly what are you doing. .obsidiancontains setting for vault and some metainfo about vault for obsidian app, so it can be tricky thing to use symbolic link.
For now, you can’t set different location for .obsidian folder in app and I believe you can’t even set location deeper that root folder of vault.