OP, your blog on pot odds is a bit off.
1. Pot odds are not just crucial when you behind in a pot. You also need to work out pot odds when you are ahead as well to make sure you aren't giving your opponents correct odds to call draws.
2. With a flush draw, you don't have 25% to hit it by the river. It's actually much more at ~35% (rounded). If we use the rule of 4, 9 x 4 = 36%, which is pretty close to 35%, but why higher than the 25% you've given. However, we only use the rule of 4 and calculate the chances of the flush hitting on the turn or river if there will be no more betting after the flop. Otherwise, we use the rule of 2 and calculate the odds off hitting on flop-to-turn. And then again on turn-to-river.
3. The odds of hitting a flush on flop-to-turn is ~19% and from turn-to-river is ~19.5%. Using the rule of 2 for each, it's 18% which is, again, very close.
4. In your example: Player has a flush draw on the flop and has to call a 2K bet to win a pot of 10K (8K in pot + villains 2K bet). This is giving the player 5:1 pot odds on a call. Since player is on a flush draw, and villain still has money behind, player calculates the odds of hitting their flush on the flop-to-turn, which is 4.22:1. Given 5:1 odds, this is profitable call. The turn is a brick and the pot is now 12K. Villain bets 4K and player has to call 4K to win a pot of 16K, getting 4:1 to call. Since the odds of hitting a flush on the turn-to-river is 4.11:1 to call, the player should fold since it will not be a profitable call in the long run.
Yes, there could be some argument for calling with implied odds, but that's something different and I want to just focus on pot odds.
5. You make a comment about pot odds not entering your thinking in the scenario and you're more concerned with opponents stack size; or rather, effective stack size but I think your mistake is not using the two together because they both go hand-in-hand.