There might be different levels of thread opt-in, prime95 might not care about other threads finding out what the 338134th digit of prime is and mark its threads as unrestricted sharable.
Apple's new hardware approach might work well for this: on the A12X chip used by the new iPad Pro, they have 4 high performance cores and 4 low power cores. Let Chrome have a couple low power cores, and that solves a few problems:
1. I get security isolation between Chrome and the rest of my apps. 2. I no longer care very much when poorly written javascript wants to consume 100% of CPU because it's only running on a low power core. 3. My battery life is also better because Chrome can't consume a high power core.
Scheduling only threads of the same process on a SMT group at a time is the easiest portsmash mitigation while still retaining some of the SMT peformance benefit.