I'm not totally sure I understand correctly:
1) a TCP packet from source IP S comes in on side A of your tunnel
2) instead of acknowledging the packet, side A only sends it as data to side B other TCP (ssh)
3) the data may get lost, in which case, the TCP connection between A and B retransmits
4) side B gets the data, forwards the packet to the destination IP D
5) D acknowledges, sends a packet to S
S --------- A ================= B ------------ D
When there is a lot of packet loss at step 3, the delay before S getting the acknowledgement sent at step 5 increases and S sees the congestion. Unlike TCP-over-TCP where A acknowledges packets from S as soon as it gets them.
Is that right?