Preheat the oven to 400°F. Lightly oil 4 ramekins/cocottes/mini gratin dishes with at least 8 oz/1 cup capacity. Place dishes on a sheet pan and set aside.
For the filling, heat the 1 tablespoon of olive oil in a large pot over medium heat. Add the diced onion and sauté until very, very soft, about 5 minutes, stirring often. Add the minced garlic, rosemary, thyme, and chili flakes (if using) to the pot and stir. Sauté until the garlic is very fragrant, about 45 seconds. Add the balsamic vinegar and stir. Add the 5 cups of diced vegetables and the lentils to the pot and stir to coat everything in the oil. Season heartily with salt and pepper. Sauté the vegetables and lentils another two minutes or so, stirring often.
Add the vegetable stock and tamari and stir. The liquid should cover all the vegetables and lentils nicely, by about a half inch. Bring the mixture to a boil and then simmer until the vegetables are tender and the lentils are just soft, about 45 minutes. It helps if you place a lid on top of the pot slightly askew, leaving a little gap for air to escape.
When the filling is done, in a small bowl mix together the arrowroot powder and cold water. Scrape this slurry into the pot with the filling and stir to mix it in. Remove the pot from the heat.
For the celery root mash, place the diced celery root and garlic cloves in a medium saucepan. Cover the vegetables with cold water/vegetable stock if you like, and then place the pot over medium heat. Bring the mixture to a boil and then simmer until the celery root pieces are tender, about 15 minutes.
Drain the celery root and garlic, and place it in a food processor fitted with the "S" blade. Pulse the vegetables a couple times to get them moving. Add the olive oil, unsweetened almond milk, and some salt and pepper. Run the motor on high until you have a cream, homogenous mixture. Check it for seasoning and adjust if necessary.
Divide the filling amongst the 4 oiled dishes. Then, divide the celery root mash among the tops of the 4 dishes, smoothing it out with a butter knife or spatula. Drizzle a bit of olive oil on top of each pie and sprinkle with salt, pepper, and thyme leaves. Place the assembled pies back on the baking sheet and slide into the oven. Bake the pies until the filling is bubbling and the tops are very lightly browned, about 20 minutes.