Trim the tops off the beets and scrub. Coat in oil and 1 tsp of salt. Add thyme and wrap in aluminum foil. Place on a baking sheet and roast for 50 minutes at 400 degrees.Halve the acorn squash crosswise, scoop out and discard the seeds, and slice into 1/2" half-rounds.Drizzle squash with oil and 1 tsp salt. Toss to combine. Roast on a baking sheet for approximately 25 minutes until golden.Combine garlic, maple syrup, almonds, 2 tsp salt, lemon zest, lemon juice, chili flakes, and vinegar in a food processor and puree until the mixture is smooth.Once beets are cool enough to handle, peel the skins away and chop.Add the chopped beets to the mixture and blend until combined. Add salt to taste.Spread the muhammara on a plate and place the roasted squash on top. Drizzle with Herby Chimichurri to finish.