Using L2TP to connect two MikroTik devices and the networks behind them is totally possible. You can do it all with static routes, a dynamic protocol like BGP or static neighbors in OSPF or a mix of that and PPP routes.
For a small or simple pair of two MikroTik devices I would suggest either all static routes or static routes and PPP routes. The way PPP routes work is that when a client connects the server adds the routes defined into their routing table. This is because the client typically injects a default route back to the server. This is likely undesirable in a site to site VPN setup so the client typically turns off the add default route option and relies on a static route specific to the networks behind the MikroTik acting as the server.
Say we have 2 devices, m1 and m2. The networks behind each MikroTik router are 192.168.1.0/24 for m1 and 192.168.2.0/24. We'll use 172.16.254.0/24 for our VPN clients, carving out a /31 to use with each pair to keep things super clean. The m1 device will be the server at 172.16.254.0 and the m2 device will be the client at 172.16.254.1 under the 172.16.254.0/31 allocation for our IPAM fanatics. Lastly, the public IP for m1 will be 1.1.1.2/30 and m2 will be 2.2.2.2/30.
For m1, configure it to be an L2TP server and setup the PPP profile and user accounts.
/interface l2tp-server server set enabled=yes use-ipsec=yes ipsec-secret=s2svpn1 default-profile=default-encryption
/ppp secret add disabled=no name=m2 password=s2svpn1 local-address=172.16.254.0 remote-address=172.16.254.1 profile=default-encryption service=l2tp routes="192.168.2.0/24 172.16.254.1"
For m2, configure it to be an L2TP client and setup a static route for 192.168.1.0/24 to 172.16.254.0/24.
/interface l2tp-client add disabled=no name=l2tp-to-m1 connect-to=1.1.1.2 user=m2 password=s2svpn1 ipsec-secret=s2svpn1 profile=default-encryption add-default-route=no
/ip route add disabled=no dst-address=192.168.1.0/24 gateway=172.16.254.0 check-gateway=ping