You know that you can turn these On and Off independent of the Layering right? If you find the HAL in the Project Explorer, under the HAL you will find alignment Labels - you can then use the Alignment Label Properties to Turn them On and Off when you don't want to see them. I use this so that I don't have to create new Layers for every set of alignment Labels that I create as I guess that is your main area of change. This is an area where we let you pick the Layer in too many places when the most common use case is to place all the labels and Ticks on a common layer - so being able to change the layer in one click on the front Tab would likely solve this issue rather than having to create a lot of different Profiles just so that you can store things on a different layer.
You can group select from Project Explorer and mass change the property of Rebuild Method to "Show Empty" for those that you want to hide
Let me know if you are changing more than Layer Settings and if you think that maybe if a set of alignment Labels is assigned to a single layer would be OK and if so then the properties of an Alignment label Set would also allow you to change the assigned layer - or when you label the alignment you just change the Layer in one location and you are done - to me that would solve this question unless you are doing more changes in the settings
Alan