Hi Mike,
The section of the wiki from which you took this quote comes from identifying a dynamics model. That is a little different from what you are doing for tuning but the comment regarding that the tune must be stable enough to fly the vehicle safely does apply in using the sysID mode in general.
Yes, you can use the analytic tune web tool with the system id mode data in lieu of autotune. But again you must be able to safely fly the aircraft with the current tune.
You could use the default tune or whatever your current tune is. Or you can start with the initial tune parameters that are recommended in the wiki. However, I would recommend that before starting to analytically tune with the web tool that you zero your Rate P and Rate D like I did in the video. It will make it easier to follow along with my video.
Regarding the SID values, for most RC sport helicopters you could use the following
SID_AXIS 1-Roll, 2 - Pitch, 3 - Yaw
SID_START_HZ 0.2
SID_STOP_HZ 20
SID_MAGNITUDE 5
SID_T_FADE_IN 5
SID_T_FADE_OUT 1
SID_T_REC 90