Basically I worked for a very small company that was in the same offices as several other similar sized companies. All those companies where on the same network and there was no distinction of who was working for which company. They all just mixed together.
No one really cared who you work for anyway since it was all owned by the same 3 people and it behaved like a single large company. Technically though it was just lots of small companies as far as the Government was concerned.
For example in the UK there are tax breaks for companies that spend more than a certain percentage of the revenue on research. Just below the threshold? Simple! Split out a research arm!
You could also avoid the issue by limiting the exemption to corporations not owned in any part by a corporation that wouldn't itself qualify for the exemption, since the point of the exemption is to help real small entities and not subsidiaries of huge publicly traded corporations.