not rules, just guidelines
the rules are only rules once you're over your AFC desperation/ overly nervousness/whatever else is stopping your success. After that, they're guidelines for how to be.
The 3 second rule is to stop guys from over-analyzing things. Will she like me? What if she rejects me? What should I say?
Once you've come to realise that you want to find out if you like her, not hoping she'll like you, the over-analyzing gradually dissipates. You'll say hi to see if she's friendly, you'll talk to her to see if she's open to meeting people/has humor/whatever, you'll ask her out to get to know her better, find out if you can tolerate her flaws, etc.
If you want to still follow the rule though, do, but don't be so strict on it. What if you see a girl 20 yards away? Are you going to count 1, 2, 3, and scream at a distance to her?? No, but you should initiate moving towards her within 3 seconds, to stop yourself from over-analyzing. She's flirting with you. Inititate flirting back within 3 seconds, to stop yourself from over-analyzing her every move. But if its 5 or 10 seconds that's fine too. Its just the longer you wait, the harder it gets.
That's what it comes down to, paralysis by analysis. So many guys suffer from it. Don't be one of them. Make your eye contact and smile, who cares if it takes 3 seconds or a minute. Just make sure you do it. Even if your target doesn't respond well, you'll still feel great, cuz you made an effort.