Thats a good one. On a purely muscle basis, its a tough call. I myself am a climber, so on a mountain stage, I would climb like there's no tomorrow. I would use gears so hard to turn so I could crack other riders both physically and psychologically while I was on the verge of cracking myself. So its only natural for me to assume the real Time Trial guys do exactly the same thing, they put an ALL OUT effort almost breaking their legs to do it, so I can imagine their legs are done for, even though its only 40km. I would lose maybe 5 min ina 40km time trial, and my legs would be "pumped" like I just did squats at the gym all day, so I cant imagine how their legs feel, after being 5min quicker! Maybe a Time trial specialist can respond

Over all though, the mountain stages are far, far, far more draining. You are talking about a good 6 to 7 hours on the bike. When I say draining, your lower back is sore, the ball of your feet are sore, the bridge of your foot is strained, your shoulders are just numb, your wrists and forearms are so tight, your fingers are crimped up, your mouth is stretched from having it open gasping for air all day for 4 hours, your eyes are sore dry and red, your dehydrated, and you cant even feel your legs really, your ribs are really sore from using your rib muscles to help force air in and out of your lungs, and your neck hurts so bad from bending it when you tuck down on the descents.
Its really just doing this for 6 hours that drains you.