I understand that to get full mtu size you MLPPP does the work but as this multi link does this mean i need tow l2tp tunnels per site to be running
Not really, there's a lot of confusion around MLPPP.
The whole idea of MLPPP is to be able to spread the traffic across multiple links without need to avoid packet ordering issues by sticking each logical flow to a single link to maintain packet/frame order (which is what bonding/teaming normally does, and which requires to understand the internal structure of the payload to be able to identify the logical flows).
The key tool to achieve that is to split the contents of the same payload packet into two (or more) transport packets which have their own sequence numbers, so the receiving MLPPP stack sends the decapsulated payload packets in the same order in which the transmitting MLPPP stack has received them.
So what MLPPP does is that it fragments the payload packets using its own means, and re-assembles them at the receiving side, and it does not depend on whether the payload protocol has (like IP) or doesn't have (like L2 protocols) its own fragmentation mechanism, nor does it depend on whether there is just a single link between the client and server or there are more. The only condition is that both peers support MLPPP. And it is implementation dependent whether payload packets that fit into the MTU of a single link after encapsulation are split anyway or whether they are sent using a single transport packet. Some implementations cut the payload packet into halves, other send the bulk via one link and the part which didn't fit via the other one.
What I'm afraid of is that the MLPPP doesn't know the actual available size of the UDP packets as the IPsec overhead occupies part of the available MTU, so instead of each payload packet being transported in two UDP transport packets, it may be transported in three, as the first MLPPP fragment may be split into two IP fragments. But I'm far from sure here, you'd have to sniff to see the actual behaviour. In any case, unless you can provide a large enough path MTU so that a 1500-byte frame along with all the additional headers would still fit (and it's [IP[ESP[UDP[PPP[Payload]]]]] in the best case, can be even worse if NAT comes into play), the best you can get is the large frames to be split into two.
Just a final woe - Mikrotik seems to have resigned on further PPP development, so it supports MLPPP as both client and server on all PPP flavors, but the actual support of multiple links is only available if acting as a PPPoE client. And MPPC (Microsoft compression) is also unsupported.