That is honestly the route I would take, have your stock one done correctly. I have just heard too many stories of body shops claiming to do one thing, but doing a totally different thing. Now, being in the business...I KNOW that it happens....a LOT.
I would not be suprised if a body shop told you what they told you, about getting a new lid. But in all actuality all they did was fill the stock holes and repaint YOUR hatch lid. Not saying that is what this guy is going to do, but it very well could happen.
If it was just the three holes for the badge, then all you would need is some body filler. Spot welding three, 1cm, holes would be a waste of time. Simple body filler would work just fine. Now the wiper hole sould be welded, that is really too large of a hole to bondo....in my opinion.
I asked today about this price, and I was informed that ANY body shop buys their products from the nearest dealer. No auto company will sell direct to anyone else. In Fords case, genuine Ford products will ONLY be sold from Ford, to dealers. Ford does NOT sell to anyone else. Motorcraft parts can be purchaced directly from Motorcraft...if you are a body shop, mechanic, ect ect. But that is typically only alts, plugs, wires, filters, ect ect. No body parts.
So the body shop would pay cost + 10%, typically. At least that is the cheapest they would get it. That would make the lid in the range of 250-280...for the body shop. And of course they mark it up when they bill it out, either to you, or an insurance company. So that would put it around the 300-320 mark.
Now, one thing did come up in my discussion. The "no badge holes" thing was the trigger. If it has no badge holes, then it is NOT a Ford product. That means it is an overseas aftermarket company, producing "OEM style" parts. Meaning it is made for the Cougar...but that does not mean it will fit and function properly. You could have leaks, bad seals, warping. Then again, you could have no problems what so ever....it's really a crap shoot.
Good luck with whatever you decide. But if it was me, I would simply get the stock holes filed and the lid repainted. That way there are no questions, no worries. I mean, even the glass swap might not go perfectly. But if you have the stock holes filled, then you KNOW you will be Ok. And you can still have your stock spoiler holes filled and re-drill new holes, that will not be a problem. I am having that done when I get my hood re-painted.