Hi,
I've used something similar to your configuration to migrate VLANs from one infastructure to another and have not encountered problems. In principle, if you are using PVST or RPVST, both links will be in forwarding state, as lon as each port has only one permitted vlan.
In both case, for the VLAN 100 and 200 there are not closed loops that trigger STP to block any port, but in the second case, is highly probable that the native VLAN will be in forwarind in 1 port and in blocking in the another one.