The Touhou series of games are independent, with all of them created by one guy (and he seems to endorse fan creations). Not quite the same as covering work from larger companies.
Speaking of larger companies, most of them are quite aware of the growing western remix scene, and are definitely aware of the huge doujin circles in Japan. They have essentially given up on taking any legal action against said doujin groups, and nowadays, even companies like SEGA are releasing remix albums at doujin events like Comiket and M3. They don't really seem to care anymore.