Shawn, the Sage migration apparently uses a couple of different indicators to tell if a 3rd party mod is installed. One is obviously the SY_Module.M4T table, if it is, like JobOps and Ascent, a separate module. Another is in SY_Enhancement.M4T. You can use Data File Display and Maintenance in the old, source system to find the enhancement record(s) in that table and easily remove them when you're getting ready to migrate. The other place that I know that triggers the warning is SY0CTL.SOA. In that file, look for records that start with 'l' (that lower case 'L') followed by the module code affected by the enhancement, or the enhancement module itself. Once you remove those records, you can probably migrate without warning.
When the time comes, I can help you if you need it. I've cleaned out a lot of trash from system tables over the years, including stuff that I put there.