This question may be related to a resolved thread.
I ran across this issue today, and simply due to lack of experience with MSM site setup and lack of correct documentation a wasted 2 hours of my day tracking this down. The above thread mentions that docs needed to be updated and that was posted some time ago. I looked through the MSM docs just to be sure i didn’t overlook it and I was still unable to locate it.
.htaccess files needs to be added to the subdomain directory when creating a new site, it can follow the same setup.
└── domain1.com
├── admin.php
├── index.php
├── images
├── system
└── themes
└── domain2.com
├── admin.php
└── index.php
└── .htaccess
Thanks.