The align tool, not one of my favourites, but.. screenshots of the steps merged into one ( Edit: Forgot to invert the layer stack 
)
(1) Is the layer stack, rubber banded to give those corner marks.
(2) Is the align tool applied, based on the image (canvas). Anything off the canvas is normally 'invisible'
(3) Just for info and useful to know, View -> Show All , will display layers that are off the canvas. It does not do anything except that.
(4) To get a strip and lose that 'first canvas' apply Image -> Fit canvas to layers and then to get a single layer Image -> Merge Visible layers. Also turned View All off.
Edit: Just had a look at your video. For that appimage launcher try out. I would go for the ubuntu version rather than the MX version. Also looks like you need fuse (fuse2) installed. That will replace fuse3, it is up to you. The other option is the flatpak.
)(1) Is the layer stack, rubber banded to give those corner marks.
(2) Is the align tool applied, based on the image (canvas). Anything off the canvas is normally 'invisible'
(3) Just for info and useful to know, View -> Show All , will display layers that are off the canvas. It does not do anything except that.
(4) To get a strip and lose that 'first canvas' apply Image -> Fit canvas to layers and then to get a single layer Image -> Merge Visible layers. Also turned View All off.
Edit: Just had a look at your video. For that appimage launcher try out. I would go for the ubuntu version rather than the MX version. Also looks like you need fuse (fuse2) installed. That will replace fuse3, it is up to you. The other option is the flatpak.