First off, why people don't run max HP chansey is beyond me. The special bulk difference is miniscule even with an eviolite and it saves you about 5% on both of those attacks.
40 Atk Life Orb Protean Greninja Low Kick (60 BP) vs. 252 HP / 252+ Def Eviolite Chansey: 221-265 (31.3 - 37.6%) -- 85.5% chance to 3HKO
It's a fine Greninja counter because it works in practice. Yes, where it matters most. Chansey just rarely gets that low, and if it does you check Gren, heal up and never get into that issue again. Gren still has longevity issues when you draw out the fight vs it. Because you're preaching about momentum, I assume you're talking a sableye team since it's really the only team that needs it to any degree... needs because sable has a sufficient lack of bulk for something with magic bounce (A consistent problem with all magic bouncers, so compared to them he is relatively bulky.). So in that scenario, where are you getting three layers of spikes? If you're using a sable team and you've let them spike you with three layers, you must be pretty damn bad.
And let's get one thing straight: Stall, by nature, is a 'momentum kill'. Don't ever think it's anything else. You can pressure, you can create switches and you can make plays, but YOU are doing that, not the stall team. Because of the inherent lack of speed, the general lack of power and the usual need for recovery, stall teams are always going to be able to be pushed on the back foot. If you think you can consistently keep pressure throughout a match with a stall team, you're dead wrong. As soon as they use U-turn, taunt, Baton pass, a boosting move or move into a threat, whatever you've been doing doesn't matter: You play on their terms because even when you do all of this, your opponent may have a mon that simply invalidates what you do. And for stall teams, that's fine because you generally are able to win on an opponent's term unless they bring stall breakers or ways to crack your team with ease. No matter what, if you don't have speed to outspeed what naturally beats your team, you don't have a chance.
So Chansey being a momentum sink? Guys, we've known this forever. It hasn't changed and this isn't a great epiphany. If you're going to be bothering with momentum, go build a voltturn team with some bulky mons. I've done it, it isn't as effective when you try to form it to a true stall team. Hence why I never pursued it heavily. Chansey may be steal your own momentum but it sure as hell does a nice job of making sure none of your opponent's special attackers GAIN any momentum. Sure, there's some special mons that give chansey hell, but very few outside of landorus, mixed thundy and taunt gard manage (which must avoid losing around 72 HP to do so).
As I said, the only stall that really cares if it loses momentum is sableye... All other stalls should be prepared to expect it... Technically, I think a sable team not prepared to expect it isn't any good, but whatever... I won't use a slower gen4 rotom- with a better ability.