First let me say that I agree that Schala is most likely the entity.
I feel that she is observing the progress of Crono's party, and opening the gates at appropriate time zones and locations, as a means to help them advance.
However, there are unknown complications with when and where she places them, surely if Schala is behind this, then we can assume that she also knows of the different branches in time that are also being erased, which is where Chrono Cross comes in. While Crono's party saved the world from Lavos in Chrono Trigger, there were certain consequences in their actions, as they also destroyed hundreds more in the process, and karma got the better of them in the end.
We also see this in the ending of Chrono Cross, Schala/Kid, does not end up living with Serge in the end of the story, we're only shown that it's possible she may have reincarnated in a different time where the two could meet. But if Schala messed with the flow of time, then she was just as guilty as Crono's party, and had to pay for it in her own lifetime.
Simply put, if Schala were responsible for the gates, then she most likely had to choose a time and a place that changed as little as possible.
It's also possible that Schala had her own reasons for picking those places, the entity clearly wanted Crono's party to see the devastation Lavos would cause in the future, and what humanity would have been reduced to.
The fact that the gate in Guardia forest is plot convenient, is in itself the evidence of intelligent design. In fact, if a gate were placed anywhere else in the castle at that time, it wouldn't have been of any positive use, as Crono didn't carry the pendent with him, so he couldn't escape from the jail through a portal, likewise Marle wouldn't have been in the party if the portal showed up right after Lucca joins him in the escape.
Someone was observing their progression, and chose the right moment, if it happened any sooner, then the party wouldn't have made the jump together, where if it were any later, then the party would have been apprehended by the soldiers.
Which brings us to the gate behind the door in the future scenario, which the party knew about for a long time before they could enter the door.
Someone wanted them spend some time in that time zone, to see what had happened, they also wanted Robo to join the party, because he would play an important part in the progression of things.
As for the gate in Medina village, it's possible that the entity just wanted to provide them with an easier means of transportation, perhaps they wanted the party to change history so the mystics (who are possibly the descendants of the surviving Ocean Palace mutants) could live in harmony with humans, and the party seeing what was going on in Medina might have influenced them to take action. It also provided them with a quick and easy alternate route to Melchior.
But considering how karma affected Crono, Marle and Lucca, what also happened to Ayla, Glen and Magus? Where Robo's existence was already in danger, simply do to the alterations made to the time lines.
Now, regarding Lavos, I don't think that he would go out of his way to enable his own end, some of the gates, like the one after Lavos crashes into the Tyranno Lair, or possibly the one that opens when Magus tries to summon Lavos, or the one in Medina village, could simply be distortions caused by the surrounding tension of the situations, and Crono's party might also be causing tears in time and space do to their altering history.
That is at least how I see it.
