How to use commercial render farms with the customized pipeline

I installed the Shotgun customized pipeline so that I can use Nuke Indie and Houdini Indie which wouldn’t launch with the out of the box web based Shotgun Pipeline. But now I am concerned that this distributed config will not work on any of the commercial render farms because I am not able to customize these render farms at all, they are as is and expect all maya, nuke, …file references to be local to the project. So am I stuck? Is Shotgun with the customized pipeline not compatible with commercial render farms?

Must I use Deadline AWS Thinkbox as my render farm for Shotgun?

Deadline works.

Not entirely sure what you mean.
Nuke Scripts made with the Shotgun Toolkit should open fine on a renderfarm as long as the NUKE_PATH/env is the same. Something that should be true for your custom gizmos etc as well.

However I was under the impression Nuke Indie doesnt support renderfarms?

I run Nuke Indie locally, but now it will launch in Shotgun Create. I run Maya on AWS through Deadline but now it can handle the very different file structure for the project that the Shotgun customized pipeline uses. Maybe there is a better way but this is the way that I found.