I will do so with my personal set of parameters since they are saved in my Harpoon.ini file.
No, little to do with the Harpoon3.ini file. Each mission profile is saved in an INI format file such as DefaultPatrol.mps or DefaultStrike.mps (One profile per standard mission type) in the Doctrine folder. The parameters in those files would be applied to missions in scenarios files from before 3.10. That's where the limitation would be. If different authors want different defaults applied to all their pre-3.10 scenarios then they will need special treatment. Scenarios created with and after 3.10 would maintain their existing mission parameters when rebuilding.
A possible solution to the limitation would be to use the scenlist.ini to allow the editor to specify a Doctrine folder to be used for each mission or battleset. This would not be an feature available immediately and would be a nightmare to maintain. Given the nature of the default profiles, I would believe you would get all your contributors to agree on one set and apply those to everybody's scenarios created before 3.10.
So to summarize:
1. The editor will be allowed to define the default mission parameters using one profile per standard mission type. i.e. DefaultGroundStrike.mps in the Doctrine folder.
2. Scenarios from before 3.10 that are being rebuilt with 3.10 would have the default mission profiles applied to them.
3. Scenarios built in 3.10 and after will maintain their current mission profiles saved in their scenario data when rebuilt.
4. A switch or Rebuild with Scenlist setting may be in order to override point #3 so the editor can apply new default profiles to 3.10 scenario missions.
If the contributors do want to have their own set of defaults applied to their pre-3.10 scenarios then you can:
1. Set up a battleset for each of them.
2. Change the Doctrine folder option in the Harpoon3.ini to something like C:\Harpoon3\Doctrine_Ralf
3. Rebuild by Battleset.
Somewhat like what you described but the change required is one setting in Harpoon3.ini and the mission profiles saved in individual files. This is an overabundance of configuration available to the user. However, if you are happy with the GE default missions then you won't have to touch them.