I can comment on a few of these, not so much giving a direct answer:
1) How do you easily migrate content (web maps, apps) between development, test and production environments? Our IT people want it to be scripted if at all possible.
There are a few approaches to doing this:
1) Python API - clone_portal_users_groups_and_content | ArcGIS for Developers
2) Distributed collaboration - About distributed collaboration—Portal for ArcGIS (10.6) | ArcGIS Enterprise
3) Using the sharing model, (share development items with a development group, test items with a test group, etc)
4) Recreate manually
It sounds like your organization would go for option 1, but keep in mind service publishing would need to be automated which generates new item IDs.
2) Governance: In a large agency such as ours, our IT people want full Software Development Lifecycle governance over Portal. My question is how do other large agencies tackle this in regards to "development" (where we are not actually coding anything for the deployment of web apps and maps)?
I'll defer to someone else, I don't have an answer for this.
3) Geoprocessing scripts on server: Where do you store your scripts (our IT people use Microsoft Team Foundation Server) for the management of said scripts, but I don't think ArcGIS server would map a script stored there... any ideas would be appreciated.
Are you talking about ArcGIS Server geoprocessing services? The scripts themselves are copied to the Servers arcgisnput directory during publishing, so the Server won't access them from the same directory that they're published from. Not sure if that gives you an answer or not.
