Hi.
I have expirience in many technologies and products.
I work with mikrotik routers about 2 years.
I installed mikrotik rb1100ax as core router for vmware virtual infrastructure. I maintain this project for a year. We continue to work on this project.
We used ipsec, vlans, vlans trunking,network isolation,pptp l2tp client-servers.
Also i setup many small routers like 750,951,2011 etc for SOHO with ppoe/pptp clients, wifi bridges, even with policy based routing from different LAN to different VPN. And Mikrotik as network controller for Ubiquiti AP.
Do you have configured dstnat and srcnat on the mikrotik?