Heat the butter and oil in a large dutch oven or heavy-bottomed pot over medium heat. Add the sliced onions along with a big pinch of salt; stir and let cook until the onions are translucent. Once translucent, continue cooking, stirring occasionally until the onions are caramelized. This whole process will take around 45-50 minutes, so be patient. If the onions start to stick, you can add a splash of water to the pot, stirring to loosen them.

Once the onions are caramelized, add the garlic and thyme. Stir to combine and cook for 1-2 more minutes. Add the marsala and stir, cooking for 1 additional minute.

Add the stock, water, salt, pepper, bay leaves, and beef base to the pot. Increase heat to high and bring the mixture to a boil. Once boiling, add the pasta and stir to combine. Reduce the heat back to medium and simmer, uncovered, stirring occasionally until the pasta is cooked through and most of the liquid has been absorbed.

Remove the pan from the heat and stir in the cheeses until melted. Add the cream and stir until well combined. Taste and season with additional salt and/or pepper as desired.

Allow the pasta to rest for 5-10 minutes to allow the sauce to tighten up before serving. If desired, top with additional cheese and garnish with more fresh thyme.