According to JAA regs. the aircraft operating under an AOC must be of the same national register as the issuing authority of the AOC. Netjets Chose Portugal, Flexjet, when they operated, chose Denmark.
If I were to start a business, I would also choose the best place for my investment to grow, which is what I'm sure Netjets did. They needed a EU member country as base.
The EU is after all a common market.
The discussion wether Portugal is this or that doesen't really matter in the end, as all these countries will have to comply with JAA regs. in the end.
When it comes to wether the company has a precence in the UK or not I'm not sure what that has to do with anything. The employment contract will usually specify which court is the authority in disputes, and one would think this would be in Portugal. If anything, Portugal being a EU member, the dispute can be brought to Brussels.
As I have said before. Read the contract before you sign it, then live with it for better or for worse, or simply get out.
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