In Windows, with IPv4 stack disabled, can I encapsulate IPv4 addresses over the IPv6 stack to reach an IPv4 host ?
If you disable the IPv4 operating system stack, it won't be able to access anything that uses IPv4.
You may use a IPv4-in-IPv6 tunnel (4in6) to access the IPv4 Internet over a IPv6-only connection, but your operating system still needs the full IPv4 stack operating locally. There were NAT-PT and NAPT-PT, that allowed a IPv6-only host to access the IPv4 Internet without using an IPv4 protocol stack, but a lot of problems were found with this approach and these protocols were made obsolete in RFC 4966.
The best transition from IPv4 to IPv6 is to use a dual stack during some time, gradually phasing out IPv4 in favor to IPv6.