Yes, these questions are absolutely relevant.
1. Online-only businesses are generally not eligible for Regional/ branch listings. The Regional/ branch lists things that have a physical presence in an area -- such as a storefront where someone might go to buy something. An online-only business is not particularly relevant to an area, so they generally are not listed in a locality. There are a few exceptions, most often when the online business is a major employer in a locality (because the knowledge would be relevant to someone looking for a job, or to someone who wanted to know the major industries of a particular town).
2. If the same people own "two separate businesses" in the same industry, we are extremely unlikely to list two different URLs for them. Their business model is irrelevant to us. We don't care whether they are targeting their marketing at the high end, low end, or left-handed Swiss cattle ranchers. If the two sites offer the same service (logo design) and are run by the same people, adding both doesn't offer any additional useful information for our users -- we consider it to be one business. We also consider it to be the owners' choice to break the navigation between the services their business offers -- and it's our choice to list their business once.
Try looking at the issue from our perspective. If the site owners don't consider the information important enough to include prominent links between their service offerings to make navigation easy for their own customers, why should we (who have no interest, financial or otherwise), consider it more important than they do, and link it from our site? And if they do consider it important enough to link prominently, then we can offer easy access to all the content by just listing the site once, and allowing surfers to use the navigation as intended by the site owner.
3. I asked about Home Work Opportunity, because it wasn't clear to me if that opportunity was to create logo design firms. And to be honest, it still isn't clear.