Reading this quote,
The 802.1Q standard defines one unique Spanning Tree instance to be used by all VLANs in the network.
STP runs on the Native VLAN so that it can communicate with both 802.1Q and non-802.1Q compatible switches.
This questions is based on 802.1D standard, How would be the behavior between two switches with ISL encapsulation, once which ISL doesn't support Native VLAN?
Beside, using ISL instead of 802.1Q, that won't disrespect the first statement?