Current trajectory planner is not suitable for any machines with non-trivial kinematics. Please take a look for the following code at getStraightAcceleration() on emccanon.cc:
tx = dx? (dx / FROM_EXT_LEN(AXIS_MAX_ACCELERATION)): 0.0;
For non-trivial kinematic machines, such as SCARA, the dx is contributed by several joints other than AXIS_0. However, the above code assume that it only depends on AXIS_0, which is not true for those machines. Therefore, the calculated accel/velocity for trajectory planner may be incorrect.
This is the comment from Alex Joni:
There are some problems in the current version of emc2, that joints (motors) and axes (carthesian directions) are mixed in a couple of places. There is ongoing work (on the joints_axes3 branch) to fix this. But it's a lot of work (in a lot of layers and places), so there is no fixed timeline when it will be useable.