There is no good way to do hardware offloading across multiple switch chips, see https://help.mikrotik.com/docs/display/ROS/Layer2+misconfiguration#Layer2misconfiguration-VLANfilteringwithmultipleswitchchips
There are also issues with Atheros fast ethernet (10/100Mbps) switch chips, they do not support hardware offloaded hybrid ports and see the comments at the bottom of the section https://help.mikrotik.com/docs/display/ROS/Switch+Chip+Features#SwitchChipFeatures-HostTable regarding mixing hardware and non-hardware offloaded ports.
Using a single VLAN-aware bridge works fine but you do loose hardware offloading, only really an issue if you have significant traffic between ports within the same VLAN