Hey folks!
Keeping variable references in sync actually comes with performance losses so it's recommended to only use the option when necessary, that's part of why it's turned off by default as well. The setting could certainly use more documentation! A number of people have expressed that keeping variables in sync is the expected behavior for them and it makes sense for that to be the case.
At the moment, though, the fix I'm aware of for the original issue is using the "Keep variable references inside the query in sync with your app" option.
@dguzzo and @Alex_Zak, would you mind explaining your use cases a bit more? Does using a JS query event handler with the setting turned on work?