There was a TNG where Data was learning to tell jokes (badly) from Tip O'Neil. O'Neil told a joke about a guy using a fish for a briefcase. Data asked what was funny about an amphibian briefcase. Fish aren't amphibians. Does Data saying that they are make it true in the star trek universe? Did they just change a basic rule in biology, or did the writers make a harmless mistake?
You're saying the time travel must be valid because we saw it in the episode. That means any mistake the writers make becomes true. If you accept that, then there's no point in talking about plot holes in the first place. Because there's no such thing.
Look at Trek XI. Nero went back in time and blew up Vulcan. So by the present its already destroyed. So why would he go back in time and blow it up, if it doesn't exist to threaten him?
If the older Odo doesn't exist, how can he sabotage the ship and prevent them from traveling back? In the show they didn't say the colony existed for a time. They said the colony never existed. That's correct, since they never traveled back to found it. But since they never traveled back, how can colonists who don't exist prevent their own existence?
Also, I don't see how using different time travel tech would change the laws of physics. Gauss' Law of Electricity is always true, regardless of what type of sensor you use to observe electric fields.