Add chia seeds, almond milk, honey, vanilla, lemon zest, and kosher salt to a medium bowl, whisking to combine. Whisk 2 more times within a 10 minute period, then cover the bowl with plastic wrap, and transfer to the refrigerator. Let sit overnight (for up to 2 days).
Meanwhile make stewed rhubarb and macerated strawberries. Add rhubarb, vanilla sugar and water to a medium saucepan over medium-high heat, stirring to dissolve the sugar. Bring mixture to a boil, reduce heat to low, and simmer until rhubarb is tender but not completely falling apart (8 - 10 minutes). You'll want to stir occasionally, but be gently when you do. Once the rhubarb is cooked, gently stir in a squeeze of lemon, then taste for sweetness. If you find the mixture to be a bit on the tart side, stir in a little extra sugar. There should be a good balance of sweet and tart. Let mixture cool completely, then store covered in the refrigerator until you're ready to use it.
Add finely chopped strawberries to a small bowl with the vanilla sugar and lemon, stirring to combine. Let sit for 30 minutes, then store covered in the refrigerator until you're ready to use it.
To serve, whisk the chia seed-almond milk mixture to break up any lumps. Taste for sweetness, and add additional honey if needed. Add 2 - 3 spoonfulls of the stewed rhubarb to small jar or bowl. Top with half of the chia pudding mixture, then finish with a layer of macerated strawberries. Repeat with another small jar or bowl. You will have a little extra stewed rhubarb and macerated strawberries. Strawberry Rhubarb Chia Cups can be enjoyed immediately or store in the refrigerator for up to 2 days.