1. No, it's disabled by default. If you enable the 's0' stp domain, only 'default' vlan will be automatically part of it by auto-bind by default.
2. This command is to configure which type of BPDU packets will be sent out of a port in a vlan. For PVST+, untagged ports should be 'dot1d' encapsulation type and tagged ports should be 'pvst-plus' encapsulation type.
# create vlan ONM tag 100
# configure vlan ONM add port 1 2 tagged
# configure vlan ONM add port 3 4 untagged
# create stpd s1
# configure stpd s1 mode dot1w # This is for RSTP
# configure stpd s1 add vlan ONM ports 1 2 pvst-plus
# configure stpd s1 add vlan ONM ports 3 4 dot1d
# configure stpd s1 tag 100
# enable stpd s1
3. You need to create an individual stp domain for every VLAN.
4. You could use the 'auto-bind' feature to add ports into a corresponding stp domain automatically.
# configure stpd s1 default-encapsulation pvst-plus
# enable stpd s1 auto-bind vlan ONM