Is there a way to control the y position of a popup?
I use a native workaround by making the whole popup transparent and slightly longer than required, with the solid “body area” positioned at the bottom of it. This allows the illusion of it starting lower down the page.
There’s probably some CSS method too, I’m not sure.
This is another basic bubble thing that would be so much nicer if they simply gave us some basic positioning options. 
@emmanuel
Bubble told me that there popup is not so well designed and has some issues. It would be better to create your own popups with an floating group to solve more weird behaviors of the default popup. And this works perfect!