Just want to echo that we, too, would like to see the auto/manual trigger "templatizable" in some fashion, or pulled out of the template all together.
I do know Thoughtworks has played with this in the past. I believe it was even in one of the releases before being pulled out again for some reason. Maybe someone on that team can add some commentary as to why this might be difficult to implement.
As a workaround, you could set all your pipelines to auto trigger and just add a dummy, manual pipeline before the ones you don't want to auto trigger. This has the potential to explode the number of pipleines you may need which increases the maintenance and related. It also could alter any stats you may be tring to extract from GO (e.g. pipeline count, success rate of pipelines in prod, etc...). We started down this route and quickly abandoned it for those reason. We just manually trigger all our deployment pipelines to every environment which isn't a big deal.
This is how the workaround would look, as an example, for clarity:
BuildPipeline(auto)<-DevPipeline(auto)<-TestPipeline(auto)<-DummyPipeline(manual)<-ProdPipeline(auto)
Dev, Test & Prod could all use the same template. The "DummyPipeline" would need to be manually triggered in order for the ProdPipeline to trigger.
The ability to templatize more than just a pipeline (e.g. stage, job, task...) ultimately would solve this as well and add more ability to reduce config size, standardize functionality, among other benefits.