Interesting question @korontari!
I'm a big fan of multisites, though I've never used them in quite the way you're suggesting.
My multisites are setup as follows:
/backdrop
/sites
/site1
/site2
/site3
sites.php
(i.e. the default way suggested in /sites/README.md)
In your case, if your server is entirely dedicated to running Backdrop sites, then it sounds logical that you'd install Backdrop into /htdocs. If you have (or want) non-Backdrop sites on your server as well, then you could install Backdrop into its own directory in /htdocs.
For example:
/htdocs
/core
/files
/layouts
...
/sites
/themes
etc.
(Backdrop installed in /htdocs)
Or
/htdocs
/backdrop
/core
/files
/layouts
...
/sites
/themes
/drupal
/wordpress
(Backdrop installed in its own directory)
Once you've installed Backdrop how you want it, you can work out how to setup your individual sites. If whatever system you're using for automatically creating subdomains based on folders works for folders other than those directly inside /htdocs, then maybe you could configure it to apply instead to folders inside /sites. Then you can just use Backdrop multisites as normal and let whatever that other system is worry about the subdomain part. If that's not an option however, then symlinks sound like they could work. In that case, you'd have something like this:
/htdocs
/backdrop
/core
/files
/layouts
...
/sites
site1 -> ../../site1
site2 -> ../../site2
site3 -> ../../site3
/themes
/site1
/site2
/site3
As you can see, it looks like in this case you'd be better off having Backdrop installed in its own directory. That'll mean you'll also have a backdrop.mydomain.com subdomain setup automatically, but I think that's better than installing Backdrop in /htdocs and having core.mydomain.com, files.mydomain.com, layouts.mydomain.com, etc.
I'd be interested to hear how you go with this, especially if symlinks work in this case. I don't believe you'd need any additional configuration in .htaccess, but then this is all in theory, I haven't tried any of it myself...
In my server setup (I use Apache and virtual hosts) I have
DocumentRoot /var/www/backdrop1
. Maybe you need to do something similar (e.g. for each site, point the server to Backdrop root, rather than the individual site directory). That way Backdrop can use its multisite feature to find the appropriate site when the (sub)domain is accessed (via /sites/sites.php).Failing that, can you tell more about your server setup? Are you using Apache or Nginx? How does the automatic subdomain thing work?