Been doing a lot of testing and posting on the MS forums. Here is what I found. If your Integration Services Server is 2016 then you need to stay with SSDT 16.5. You also need SSMS 16.5 installed as well. When You deploy a package within SSDT it needs to use the 2016 isdeploymentwizard.exe . 
if you want to read some of my testing details. Here is a link. https://social.microsoft.com/Forums/en-US/2710aac7-e896-48b1-9904-49dac98506e1/weird-depolyment-issue-with-package-with-a-script-task?forum=sqlintegrationservices

but for everything to work correctly I downgraded SSDT to 16.5, install SSMS 16.5 and if you install SSMS 17.x + there is no issues but you have to keep 16.5 installed.

Ok I have downgraded to SSDT 16.5 and Currently have SSMS 16.5 and I can deploy Packages now from SSDT.

If I deploy the Project in SSDT 16.5 the script executes

If I deploy the package in SSDT 16.5 the script execute

If I deploy the package with SQL 2016 isdeploymentwizard.exe the script executes.

So this is exactly what I want to work. Shame upgrading the SSDT breaks the package deployment for Integrations Services 2016.