[DahkCeles]

I had more time to do some toying around, and here's a simple solution. I believe the flight paths are already marked, just invisible and changed to a different icon. They appear briefly when you mouse over other paths, if it requires going past a location you haven't discovered.

So the solution is just to make them appear, and stop the game from re-hiding them.

-- Step 1: Wait for the flight map to be created
-- Step 2: Any time the flight map appears, enumerate through every flight path pin
-- Step 3: Make each pin shown, and prevent the the OnMouseEnter/OnMouseLeave events from overriding this
 
 
-- STEP 1:
local alreadyHooked
hooksecurefunc("FlightMap_LoadUI", function()
    if (alreadyHooked) then
        return
    else
        alreadyHooked = true
        
        -- STEP 2:
        FlightMapFrame:HookScript("OnShow", function()
            for pin in FlightMapFrame:EnumeratePinsByTemplate("FlightMap_FlightPointPinTemplate") do
                -- STEP 3:
                pin:Show()
                pin.SetShown = pin.Show
            end
        end)
    end
end)

PS. This is the complete addon, minus the TOC file of course. I tested briefly with an alt who had a couple unknown flight paths and it seemed to work.