Using the Tool
You can find the tool in Plugins -> LODOptimiser Content, you'll see a LODOptimiser widget. Right click that and hit Run Editor Utility Widget
This is subject to change, I will move this to the toolbar at some point.
Now that you know how to open the tool, lets get on to using it. With the LOD Optimiser open, use your Content Browser to select your meshes that you want to set Min LODs for per Quality Level. Like so:
NOTE: You can use Skeletal Meshes too (NOT Cloth Assets), I am using Static Meshes here as a reference.
Then, navigate back to the LOD Optimiser tool and you should see that there are meshes selected and the Apply button is no longer grey.
Now, set the minimum LOD that you want a Model to use for each certain quality level.
NOTE: The numbers are not the MAX LOD a Model can go up to, but rather, the lowest it can go. For example, if you set a model to have a min LOD of 3 at Low quality, it will always render at LOD3 or Higher (LOD4,LOD5,Etc). This is effectively an Asset Quality.
Now, hit Apply, and you'll see all the meshes have now been updated!
NOTE: The LOD Optimiser tool will limit itself (per mesh) to the number of LODs specified by a mesh. For example, if you have one mesh that has 2 LODs and one mesh that has 4 LODs, you can still set the Low Quality's Min LOD to be 4, and the mesh with 2 LODs will have it set to 2 instead of 4. You don't need to worry about applying in several batches for meshes that don't have the same number of LODs. This is shown below.
One thing you may notice is that, if you're using the Mesh LOD Colouration mode, when changing your Scalability settings, your LODs aren't changing. This is because Epic made it so Unreal doesn't use the Quality Level for Static Meshes with the Scalability settings (For reasons unbeknownst to me). You have to manually call r.StaticMesh.MinLodQualityLevel <0/1/2/3/4> if you wish to view it correctly.
You will also need to set this up via some form of settings, or, add it to your DefaultScalability.ini file (setting it in your DefaultScalability.ini file will allow you to easily preview changes in-editor when changing scalability).
Every time you make a change to a mesh with this tool, you will need to re-run the command again (if you set this via DefaultScalability.ini, just change your quality level to something else then back to what it was).