I put in a vote for 'yes' because in practical terms, yes. ...In technical terms what I actually use is 'addskillpoints' from console commands.
Generally sparingly - for example, my initial run through the game, I ended up giving myself exactly one extra skill point so I could take both shield & phase ship skills. Technically cheating? Yes. But in practical terms, those skills will never both apply to the same ship, so all I'm really doing is giving myself the freedom to pick what my flagship is without having to spend two story points every time I want to try out a phase ship when I'd been using regular ships or vice versa.