The following video best demonstrates these three, but to sum it up: 1.) An adjusted route to take is to go for the early damage upgrade after beating the Yellow boss and then perform Nightskip. This will make the Venom fight quicker to finish and saves around 11 seconds. 2.) After defeating the Red boss in the Sewers, go to the Downtown entrance at the top of the map, enter the door to the left and use Nightcrawler's teleport ability to reach the other Downtown entrance quicker. Saves about 12 seconds. 3.) Using a combination of the Black Suit's slam attack and air dodge (alongside direction input to the left) at the highest part of the Pier map, you can "fly" towards the top entrance to Downtown (normally inaccessible after beating the Pier/Blue boss) and make your way to the Flying boss, skipping both preceding fights and having to do Downtown shortcut (one of the most difficult tricks for this game). Adjusted routes need to be taken to avoid triggering the two skipped fight sequences in Downtown, tallying to 24 seconds shaved for Any% and 17 seconds for NG+ (when compared to previous runs that used Downtown shortcut).
In total, Any% can be cut down to 47 seconds and NG+ in 29 seconds.