If someone is on your machine and you don't know it, they don't have to use side-channel attacks.
They'll can just use any of the thousands of other ways of privilege escalation to read the super-secret information you have stored in RAM, or find it when it is written to disk.
The OpenBSD folks disabled SMT by default because of TLBleed.
A non-datacenter/cloud user disabling SMT to avoid TLBleed is like a normal person carrying a fireman's rescue saw around with them 24 hours a day in case they get into a situation they have to saw themselves out of.