The rules are simply not going to answer all of your questions here, unfortunately. Some things you will have to ask your GM to rule on for your own game.
You can avoid a lot of headaches, though, and figuring out answers to questions the rules don’t address, by just letting the gelatinous cube engulf the target itself, so I have detailed how that works first.
Can I ready an action to use bottled ooze to interrupt an opponent? Yes.
The good news is that the rules do support a way to have the ooze interrupt someone’s movement and try to engulf them. This is how this idea “should work” under the rules. There’s arguments to be made for alternatives, but as a GM I might just say you should do things this way to avoid having to have those arguments.
When the alchemist activates the extract, [...] the ooze [...] attacks the closest creature. The ooze is [...] treated as a summoned creature.
The ooze is going to act immediately when you throw the bottle. This is consistent with being treated as a summoned creature—summon monster and summon nature’s ally both say “[the summoned creature] appears where you designate and acts immediately.” So you can definitely ready an action to summon the ooze next to someone, and when you do, the ooze gets to act and attack, probably using its engulf attack, immediately. The person only gets to resume their movement after that—and won’t be able to at all if the engulf attack is successful.
So that much is good—it’s not exactly the sequence you describe in your question, but it is a way for the gelatinous cube to grab someone in the middle of whatever they were doing. It takes up the gelatinous cube’s turn, but that turn happens immediately so that’s OK.
Can I just summon the gelatinous cube in the space the person is already in? No.
You didn’t ask, but just to be thorough: yes, you need some kind of trickery to get someone into the bottled ooze, you can’t just summon it already engulfing someone.
A creature or object brought into being or transported to your location by a conjuration spell cannot appear inside another creature or object, nor can it appear floating in an empty space. It must arrive in an open location on a surface capable of supporting it.
Since a bottled ooze is “treated as a summoned creature,” and summoning spells are conjurations, the ooze cannot be thrown into an occupied space.
Can someone (accidentally) run into an ooze on their own turn? Yes.
The transparency ability describes this, saying
Any creature that fails to notice a gelatinous cube and walks into it is automatically engulfed.
Can I ready an action to create a hazard someone is “about to” run into? Yes, but they can always stop or go around.
Quite simply, someone is either in one square, or another square. There is no “in between” point under the rules, and a creature is never committed to continuing to move forward. If you create a hazard in front of them, they can always stop. In most cases, they can also choose to change course and go around it (though they cannot if running or charging, since those are required to be in a straight line).
Your GM might, as a houserule, choose to make this kind of thing a Reflex save instead of creatures simply being able to stop at a moment’s notice, but whether or not to do that, and what the DC should be, is going to be totally up to the GM. There’s no rule saying that a creature has to make a Reflex save for this.
Does transparency apply here? Unknown.
Choosing to avoid a square requires that someone be aware of the hazard in that square, so a Perception check might apply. It’s not clear if “reconsitut[ing] itself” as bottled ooze puts it counts as “moving,” so again you’ll have to ask your GM about whether or not the transparency ability applies. To me, I would guess that there is some motion involved in the sudden appearance of a 15,000-lb. ooze, but that’s just me.