RFC 6303 section 3 explains that

   The SOA RR is needed to support negative caching [RFC2308] of name
   error responses and to point clients to the primary master for DNS
   dynamic updates.

Now SOA RR owner name matches query name so it can be cached.
Using zone name as owner would be more difficult so it is left for
further optimizations.

I've verified that nsupdate correctly determines that master name
does not exist and stops update process.