>The lack of support of industry standards in pretty common
Neither spanning tree (802.1d) nor RSTP (802.1w) have any concept of VLANs. Certainly, neither standard is "per-VLAN". Both standards require the packets to be transmitted without tags.
Some vendors, like Cisco Enterprise, chose not to follow the standard and changed it to transmit the packets on all VLANs. I believe Cisco Enterprise did this to improve load balancing - but this problem no longer exists now that we have channelling technology (and have done for many decades now). So it is solving a problem that no longer exists, but they can't go back now to following the standard without causing major breakage.
Meraki came into existence after this problem was solved. There is no point in getting them to also break the standard to solve a problem that does not exist.
MST is multi-instance, not per VLAN. If you map an instance per VLAN you'll get this impact, but I don't know of any site that actually takes it to this level. You might put downstream buildings or groups into an instance, but not per VLAN.