No, this doesn't work, at least with normal routing gear.
IPv6 subnets are ALWAYS exactly 64-bits, and the routers know it (actually, the IP stack in the OS usually knows this). Sure, with some linux routers you can hack things up and sort of get that to work, but it really screws up more things than it can help.
I'm not really sure why I would need multiple subnets in my home, and go through the expense of having routers to separate them and separate WiFi APs for each.
If you just want "logical separation", or something to ease your firewall rules, you don't really need a separate subnets.