I'm using 4.12.2 patch and the latest version of Dgen. Is there a way to generate a campaign that uses beacons for radio navigation? Or is radio navigation a feature that can only be put in a mission manually with the FMB?

Copy your DGen folder and store the copy in a safe place. This way is something breaks or I am wrong you can replace the altered files with the original files.
Default Location: C:\Program Files\Ubisoft\IL-2 Sturmovik 1946\DGen <-------- Copy the DGen folder

DGen uses templates to generate the missions. There is a Red and Blue .mis file for each campaign. Altering those templates using the FMB should allow you to utilize the Beacons.

Example templates in the DGen folder:

• BerlinBlue.mis
  This is an Axis template
• BerlinRed.mis
  This is an Allied template.

Altering the templates;

• First you will need to move or copy the templates you want to alter into the Missions folders.
  Default Location: C:\Program Files\Ubisoft\IL-2 Sturmovik 1946\Missions
• Start the sim and open the FMB.
• Find the Blue (Axis) template and open it using the FMB.
• Add the number of Beacons necessary to have one at each Airfield plus any other location where you want one shown.
• Save the template.
  (Make sure not to change the name of the template.)
• Add the Beacons to the Red (Allied) template so they will work when you start a campaign as the Allies.
• Save the template.
  (Make sure not to change the name of the template.)
• Copy or move the altered templates back into the DGen folder
• Start the sim
  • Generate a new campaign
  • Continue an existing campaign and see if the beacons are shown.
    (You will need to complete the mission it has already generated before you will know if they beacons have been added.)

If you want to continue an existing campaign make sure to add objects to the templates only. If you re-number the existing objects or delete objects from the templates you could cause existing campaigns to quit working.


Wheels

Yes and no.

If you meant a "switch" or option of sort to activate in game to get beacons in a existing dgen campaign, answer is no. As mentioned by Wheels, they must be already set within mission templates (the "Blue" and "Red" .mis files); these latter can be altered only by editing in FMB. To do this, you must copy files inside the mission folder (FMB cannot access to dgen folder) and, when done, copy the modified version again into dgen folder, replacing old ones.

Would be great if some campaign builder would make some dynamic campaign including this feature, but so far (AFAIK) none did.

Be sure to read carefully specific instruction which came with version 4.10 of the game (section: Navigation improvements) and watch carefully this video:

Thanks a lot for the info! Very useful and very thorough! As soon as I have some time to spare (RL calls...) I'll give it a shot and see what happens.