While the pasta boils, sprinkle bacon pieces evenly in a large skillet. Turn heat on to medium-high and cook until bacon is browned and most fat has rendered.
Remove bacon to drain on a paper towel. Remove skillet from heat and drain bacon fat, keeping 1 tablespoon of fat in the skillet.
In a food processor or high-speed blender, add the butternut squash, garlic, 1/2 tsp salt, 1/2 tsp pepper, 1/4 tsp red pepper flakes, and 1 cup of pasta water.
Blend until sauce is smooth and creamy, scraping down sides and reblending until squash is pretty much pureed. Add in egg and pulse a few times until egg is integrated into the sauce.
Return skillet with bacon grease to medium-low heat. Add in cooked pasta and about 1 tablespoon of remaining pasta water. Toss with tongs until pasta is heated through.
Turn heat to lowest setting. Add in butternut squash sauce and toss with pasta for about a minute, until the pasta starts to soak up some of the sauce.
Remove skillet from heat. Stir in parmesan and most of the bacon. Add in more pasta water if the sauce is too thick.
Garnish with the remaining bacon and lots of extra freshly cracked pepper. Add fresh sage, if desired.