After a closer look it seems that those elements are never on top, even when I set Top Silk to active layer for editing. They just become visible. PCB looks fine in the photo preview mode and also the gerber files are OK (except bottom layer gerbers are mirrored which isn't accepted by some PCB manufacturers but that's not related to the issue).

This is a bug in the way manually placed lines on the silk layers are shown. They are placed behind both top and bottom layer copper (and possibly inner layers: I have not checked) but above copper areas on any layer. They are not affected by the **Align > Bring to Front** tool on the top toolbar. I have raised a Bug Report.

Looks like this applies only to lines as I also have text and images that are on top.

>except bottom layer gerbers are mirrored which isn't accepted by some PCB manufacturers All most all of the PCB houses we know accept the mirror, few accept not mirror. The text problem on your case is not a bug, but a design aim. We know this problem, and can fix it not very difficult. But if we fix this, the editor will be supper slow. So we must make a choose, faster but text and other layer maybe on the right position on viewer, but right on gerber. or supper slow on every operation but good look. Try to use the layer tool, switch will make it better.

About the mirrored bottom layer might be my mistake. I haven't ordered PCBs in quite some time. The hand made lines on TopSilk become visible when I hide some other layers and select that one for editing so it's usable, but in some cases it becomes a little difficult. Like when I am trying to align what I am drawing with some footprints. I'm sure it can be fixed without slowing down the tool significantly but it probably isn't really easy to do. Anyway it's good that everything is fine in the gerbers. Yesterday though I was able to reproduce the bug where all components and top layer disappear from the layout completely (not existing at all, not just hidden) and update from schematic doesn't help. Crash recovery can return the most recent working copy. Still can't figure out what exactly triggers the bug.