I also use separate branches for Trellis and Bedrock with my own customizations, which I use as boilerplates for starting a new project. Down the road for any of my projects, if I need to update and get the latest version for either Trellis or Bedrock, I either commit or stash my edits, and git pull --rebase from either Trellis master or my custom branch so my edits are always on top. I was having a similar discussion recently.
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