I have an idea to explain how Magus's gate worked, since it seems to be a 1 way gate, or a 1 time gate...somehow. It also explains how the Gurus got sent to their time periods. We know that in nature that things travel along the path of least resistance. If you look at a picture of lightning you will see that it does not travel in a straight line, but it zig zags. It does that because if follows the path of least resistance through the air (and at a ridiculously fast rate too). The one time gates that sucked up the Gurus and the people at Magus's castle didn't have a counter gate (that's what I'm going to refer to as the gate you'll return through).
Take the gate at Leene's square in 1000 AD and you'll end up in the canyon that was there in 600 AD. That canyon gate is the return gate, because you can go through it again and end up in Leene square. We all know how the Guru of Time ends up at the End of Time, the place of least resistance when 4 or more people from the same time period enter a gate. So my idea is that when there is no return gate then you get deposited at a timeline of least resistance. The gates, which allow for travel through time, probably weakened the uniformity and stability of the timeline (if the timeline were to be represented by a piece of bread, then a gate from one time to another would be like a tiny tunnel going through that piece of bread). Therefore those weakened points would be the easiest locations for a person traveling through time to end up.
Either the Entity determined where the Gurus would end up (giving it some insane foresight...and hindsight in order to save itself) or their locations were arbitrarily determined by nature. It makes more sense that it would be nature since we're already told about the path of least existence to explain why your party ends up at the End of Time to begin with.