I'm still confused as to what to pick really.
I have a QHY5 (guider) connected to the HEQ5 mount via the ST4 cable.

In Ekos, do I pick Via: QHY or Eqmod ?
stellarmate.com/support/ekos/guide.html

I prefer via mount. Primarily it is one less cable to manage. But also if using an external guider like PHD2, PHD2 becomes aware of the mount's position and pier side. Which is beneficial for calibration.

Via QHY since you're using ST4 cable. Personally, I guide via EQMod and got rid of the cable as Andrew did.

Is there an advantage doing one over the other one?

Hi. To have the choice and try out eqmod, you'll need one of these . Lose the st4 cable and instead of connecting the camera to the mount, connect the mount to a spare usb using said cable.
HTH

I would recommend trying both methods to see which one works best for you. If you want to guide using an st4 cable through the auto guide port that is using “via qhy” but if you want to guide using pulse commands and avoid the st4 connection that is “via mount”

For almost 10 years (including the time before I used KStars), I was using the “via mount” method of sending guide commands through the mount connection since I figured since it’s already connected, why would I need another cable?

But then I did a side by side test where I tried calibrating and guiding using each method. I found that with my mount and my setup that it seemed to be more responsive and guided with less error using ST4 instead of pulse commands. But it was not a scientific carefully controlled test and it was just testing my setup. So I would recommend trying each yourself

On my H-EQ5 pulseguide works better than ST4 but on my Vixen GPD2 it's the opposite, I "feel" the mount more responsive to ST4. It's also much more stable.
I have tried also no Orion SVP and LXD-75. Same results.
It varies from different mounts and mesh/wheel/backlash combinations, so, I would try both and see what is best for you.

My EQ8 guides better via Lodestar than EQMod, so here is my result from this evening.
Best guiding for me is via Lodestar and ST4 and guiding with box size 8, the second best guiding is via Lodestar and box size 16 and the 3'rd best is guiding via EQMod, the difference is not very big and it doesn't show any difference in my images.

Br,
/Markku

Have you tried EQMod with box size 8?

There is a slight advantage latency-wise in using ST4 via camera compared to EQMod as each pulse command incurs communication latency which is smaller when using direct USB connection like cameras use instead of mount's 9600 baud serial so the corrections get applied a bit faster. Using EQDir cable command latency is around 15ms, via BT dongle around 50ms so doing corrections shorter than that just isn't possible, which is why I added filtering for short pulses in EQMod driver. In practice one less cable is usually a bigger advantage though

I did try that a couple of days ago but I think the sky was too unstable, that made the star jump around too much and made box size too small to keep the star in place, but I'll try that next time clouds go away and post the result.

Now I have some more results..
This guiding is 600 seconds at Triangulum galaxy like the others, except the guiding was done via EQMod and boxsize 8, the sky was pretty calm but the guiding shows some strange behavior.
Also there comes a lot of messages in the EQMod mount tab when guiding via EQMod..
....
2018-10-18T19:52:30: [WARNING] Warning: Invalid parameter -> Can not change rate while motor is running (direction differs).
2018-10-18T19:52:19: [WARNING] Warning: Invalid parameter -> Can not change rate while motor is running (direction differs).
2018-10-18T19:52:09: [WARNING] Warning: Invalid parameter -> Can not change rate while motor is running (direction differs).
2018-10-18T19:51:57: [WARNING] Warning: Invalid parameter -> Can not change rate while motor is running (direction differs).
2018-10-18T19:51:45: [WARNING] Warning: Invalid parameter -> Can not change rate while motor is running (direction differs).
2018-10-18T19:50:49: [WARNING] Warning: Invalid parameter -> Can not change rate while motor is running (direction differs).
....