What is the current mode Spanning Tree running on Switches, since 802.1W was incorporated into 802.1D-2004? Even being 802.1D or 802.1W still not support VLANs, just Native VLAN has one SPT instance?

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That will depend on the switch vendor, switch model, and software version which the switch is running.

When a new standard emerges, it can take some vendors a while to update their code to support the new standard. If there are switch model which the vendor no longer supports, they may never be able to support the new standard. The default STP version for a switch is also dependent on the above criteria. Most of the switches that I see actually default to the oldest standard and only use the newest standard when specifically configured to do so.

Even if a vendor updates the code for a switch model, many switches of that model, already released into the wild, may never get updated with the code necessary to support the new standard.

Most of the time, switches which are connected will drop to the newest STP standard that all the connected switches support. This isn't guaranteed, especially with heterogeneous implementations, but I have seen it almost always work that way. For instance, if I configure 9 out of 10 interconnected switches to Rapid STP, but the 10th switch doesn't support Rapid STP, the 9 switches configured for Rapid STP will have that configuration, but will actually not use it.

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