I tried this - brand new install of TDP 3.8 on Windows 7 x64 with a brand new automation script written from scratch in TDP 3.8 on Windows 7 x64.
As I typically do, I develop the automation scripts on my local machine first, save them to a network share, and then RDP into our automation host machines, open the scripts in TDP and then schedule them.
On both installs of TDP 3.8 I had done as you suggested - I ran the Configuration Wizard and instead of choosing “Custom” like I normally do, I instead chose “Toad for Oracle” (as I use that quite frequently as well).
Created my automation script, saved it, and as soon as I opened it on the other machine and clicked the “Select to File” activity, what should appear but the @#$&% Navigation Manger.
So it doesn’t appear that this solution works…