I was told a clause was unenforceable, and used the reasoning "So we can remove it from the contract?" and they wanted me to work with them so they took it out.

My usual approach with NCs is to reign in the scope of them. I've had some that could be interpreted I couldn't write any software for anyone else for up to a year.

Companies have a way of shitting their pants, and walking away from the employment offer if you question even a line or two of the "formalities" they expect you to unblinkingly sign.

I would consider that a bullet dodged.

True but it grinds the gears nonetheless (especially when considerable time has been invested, and you were actually kind of interested in what they were doing).