Thanks!
When you go to the past, you are able to change things that later influence the level in the present and help you finish it. But you can’t finish the level in the past, so in order to go through the yellow portal, you need to be back in the present again.
And about the trees: You can place them at different spots, but you don’t need to do that in order to finish the game as we haven’t fully implemented the obstacle you were supposed to block with the trees.