1) Heat a pot of salted water to boil for the pasta. Add pasta and cook to al dente.
2) While pasta cooks, heat a medium, heavy-bottomed pot over medium heat. Add the oil and butter. When the butter melts into the oil, add the thyme (optional) and grated onion (use mini food processor to grate onion if you have one).
3) Cook the grated onion in butter and oil 1-2 minutes, then add flour and cook together for 1-2 more minutes. Whisk in stock, then combine with butternut squash (drain off extra water first if using frozen) until warmed through and smooth.
4) Mix yogurt and milk together in a measuring cup first (or use 1 cup cream) then stir in and bring sauce to a bubble. Stir in cheeses and season to taste. Taste to adjust seasonings.
5) Drain cooked pasta well and combine with sauce. Use a slotted spoon and serve immediately. It can be a bit runny at first, but as it sits the extra liquid gets absorbed. Enjoy!