MMF is fundamentally designed to be framerate dependent. You pick your framerate (eg. 50fps) and 'machine independent speed' skips drawing if it can't hit that rate. Since you need to get the logic running at a fixed rate to make a framerate dependent game keep running at the same speed, if your computer still can't hit that framerate, the whole game slows down anyway, kind of defeating the point of the option. As far as I know, you can't V-sync and have machine independent speed on in MMF (or if you can, your game will change speed depending on the framerate, I guess).
If you turn on V-sync in Construct, it won't skip drawing the screen, but instead the value of timedelta increases since it's taking longer to process frames. This can result in objects 'tunnelling' through each other, or physics going a bit funky, at very low framerates. The solution is to use the minimum framerate option. It does make the game run in slow-motion if your CPU can't keep up, but so would 'machine independent speed' if it were in Construct, and hey, you can't do an infinite amount of processing and keep the same framerate.
Physics is processed on the CPU so the CPU will be the cause of the slowdown. In this case drawing the screen takes a comparitively little amount of time, so skipping drawing the screen won't solve this problem. You need to use less CPU!