The way to do this is taking out everything that has nothing to do with the problem - a router with minimal configuration.
I already wrote why this is impossible.
I also tested on RB3011 with simple configuration and sent them the result, but they ignored it for contrived reasons.
Usually Mikrotik support tries very hard to solve problems.
maybe, if the problem is simple and they can solve it. if they cannot solve the problem, they keep it quiet or refuse to admit it.
If the next problem solving step can't be done, then it will not go much farther than this. If support asks You to do something, there is a reason. Even that "stupid" question "Is it on?" is a valid one. The number of calls I got, that where just something turned off... even when they say "Of course is on!". No, not always.
And we see, time and again, huge threads about very complex problems here on the forum. Sometimes Mikrotik support take their sweet time - but they are like a bulldog with a bone: they chomp it, and don't let go.
True, sometimes they answer "No, will not fix it until v7", or "will fix in the future" - and future is one year from now. These are the "suboptimal" (the awful ones, really) answers - but one answer nonetheless.
I went looking into your post, and the formatting of the CCR iperf results made my head hurt. Please, put that mess in a sane formatting.
One iperf3 testing, from one PC to another.
PC -> hEX (IPSec/L2TP) -> internet -> 1100AHx2 (IPSec/L2TP) -> PC
[ ID] Interval Transfer Bitrate Retr Cwnd
[ 5] 0.00-1.00 sec 10.8 MBytes 90.9 Mbits/sec 80 131 KBytes
[ 5] 1.00-2.00 sec 4.97 MBytes 41.7 Mbits/sec 108 49.9 KBytes
[ 5] 2.00-3.00 sec 5.53 MBytes 46.4 Mbits/sec 25 59.9 KBytes
[ 5] 3.00-4.00 sec 5.47 MBytes 45.9 Mbits/sec 27 68.6 KBytes
[ 5] 4.00-5.00 sec 5.47 MBytes 45.9 Mbits/sec 34 53.7 KBytes
[ 5] 5.00-6.00 sec 5.47 MBytes 45.9 Mbits/sec 15 63.7 KBytes
[ 5] 6.00-7.00 sec 4.97 MBytes 41.7 Mbits/sec 15 79.9 KBytes
[ 5] 7.00-8.00 sec 5.53 MBytes 46.4 Mbits/sec 40 62.4 KBytes
[ 5] 8.00-9.00 sec 5.47 MBytes 45.9 Mbits/sec 18 71.1 KBytes
[ 5] 9.00-10.00 sec 4.97 MBytes 41.7 Mbits/sec 24 53.7 KBytes
- - - - - - - - - - - - - - - - - - - - - - - - -
[ ID] Interval Transfer Bitrate Retr
[ 5] 0.00-10.00 sec 58.7 MBytes 49.2 Mbits/sec 386 sender
[ 5] 0.00-10.04 sec 57.7 MBytes 48.2 Mbits/sec receiver
1100AHx2 is on RoS 6.47.1
hEX is on RoS 6.47.7
One link is 60/60 Mbps
Other link is 90/90 Mbps
Latency is about 10ms
I know, You want better speeds than this. Problem is: I don't have a faster link to test it. But getting almost 50Mbps from a 60Mbps limit is good enough for me.