OK, so now the following question is why exactly do you need the VLANs. This way (the port for each PC on the central router has its own bridge tunneled to a matching bridge on the server side), the traffic between each PC and its respective server is logically separated from the traffic between the other PC and its respective server to exactly the same extent as if they were using two distinct VLANs on a single set of interconnected bridges. On the transport side, the proper mapping of the client side bridge to the desired server side bridge is ensured only by L2TP username and password since you let RouterOS create the IPsec configuration dynamically, which means that all clients must use a common pre-shared key; if you wanted more robustness against misconfiguration or even intentional hacking on client side, you’d have to configure the IPsec layer manually at least at the L2TP server side, but that would still only work unless configuration for one BCP client would leak to another one.
Just adding VLANs to the protocol hierarchy at transport side would not help much as you can only configure a single L2TP server that listens on all interfaces, so if you wanted to connect every BCP client to an access port to another VLAN as a way to prevent linking incorrect bridges on client and server side (because the hacker would have to change the PVID on the access port of the “core” switch in order to connect to a “wrong” VLAN, not just the configuration of the client), you would have to use PPPoE for the transport layer, as unlike L2TP, the PPPoE servers can be instantiated and linked to individual interfaces (in your case, VLAN ones). But then you would still have to use L2TP over IPsec to convey encrypted BCP because you cannot encapsulate PPPoE into IPsec, only vice versa.
All in all, it seems to me that you have some idea regarding the VLANs that is so far away from my way of thinking that I cannot grasp it. So if you think it is worth the effort to make me understand it, we can switch to a more interactive way of communication, using the guideline here.