I've only encountered this in Nullius, but it would happen with any mod that has its own (or heavily modified) tech tree. Even with the Disable all technology requirement changes setting on, the rail block visualizer shortcut remains disabled despite having researched railways and trains (I suspect because the tech name in the mod is different and I started the game before enabling the setting). Why is it necessary to disable the shortcut at all? It doesn't free up space in the shortcut list, but it does cause confusion as to why it's still disabled even when the base is covered in train tracks.

I'd like to suggest removing the technology check entirely, making the shortcut always enabled.

Alternatively, a console command to manually enable shortcuts could be a helpful workaround.

Also affects the various blueprint shortcuts. Using IR3. +1

First of all sorry for the late reply! I got a vague idea why this might happen, but this might take some time until I can find a solution. If you got a save file with this issue, it would be really helpful sending it to me. In the mean time you can enable a specific shortcut with this command:

/c game.player.set_shortcut_available("rail-block-visualization-toggle", true)