Hi Christian,
The ZPlugin below should be what you are looking for, if not let me know.
There is one button, Stop Layer Recording, and three switches that determine if all subtools should be affected, if visibility should be turned on (done before baking), and if Bake All should be applied.
I still need to add some conditionals, like testing if the subtool actually has layers. Right now I am just assuming all the subtools are polymesh subtools.
The TV_TT2LayerRecording.zsc file and the accompanying folder should be placed in the ZStartup/Zplugs folder. Restart ZBrush and the zplugin can be found in Zplugin > Tiny Tools 2.
Hi Marcus,
It was not that difficult to detect which layer is recording or which ones are hidden. All it took was an unlimited supply of coffee, two packs of smokes and afterwards a trip to the local psychologist. Easy-peasy 
Due to the way the Layer scrollbar displays the list of layers and how ZBrush searches for UI pathnames, it is possible to detect which layer is currently recording.
It goes like this:
Set the layer scrollbar secondary value to 0. Now only the last layer is displayed on the list of layers. We know “Tool>Layer>” + the title of “Tool>Layer>Layer Intensity” is the UI path to the currently selected layer and we know that ZBrush stops at the first UI pathname it finds. Therefore we can check the [IGetID,…] of the selected layer, make sure it is not 58 (the Layer Intensity slider) and if modget = 3 it is recording.
It does not matter if all layer names are the same.
If no layer is recording you again set the layer scrollbar secondary value to 0 and then manualy Tool>Layer>SelectDown to the last layer. Now you can modify each layer. By increasing the layer scrollbar secondary value and pressing Tool>Layer>SelectUp you will always find the topmost layer of the displayed layer list.
The only problem would be if initially no layer was selected. But as far as I know there is always a layer selected. Well apart from this little bug; create a single layer, turn off recording, delete the layer, undo the delete. Now you have a single layer but it is not selected ! But that should be a very rare occurrence and does not happen when there are two or more layers.
Cheers,