Hello,
JoomSEF SOBI2 plugin creates URLs always based on original URL. This means that if non-SEO URLs for what you have as mydomain/1st sub category/companyA and mydomain/companyA are different (see it in URL editor/viewer) the resulting URL cannot be same.
The only way I see in such case would be creating a 301 redirect from one to another. But that would have to be done manually, which is probably not accpetable.