As a Sr master Ford certified technician, with 2 years college in the Ford ASSET program and over 10 years experience, this makes my brain hurt!
That being said, I personally have never seen condensation cause a problem in any turbo system. Ford has been using air to air coolers since 1998 on diesels and before that in a couple turbo cars. If you make even the tiniest hole in the charge air system you will get reduced power from a boost leak. It would be ok if you really think this is an issue to drill the hole and tap some threads in it, but as I said, I have never seen this issue. If it is happening with a eco-boost building low boost pressure, wouldn't it happen worse on a power stroke building upwards of 40psi of boost? I would lean more towards fuel system, or exhaust system (ie cats restricted.)