Beginner question:

The Ekos documentation at stellarmate.com/support/ekos/guide.html says: "Set binning to 2x2: Binning improves SNR and is often very important to the success of the calibration and guiding procedures".

There are a couple of current threads over at CN where multiple people say one should never bin the guide camera. Is this a case where the CN comments are assuming PHD2 and the Ekos guider is different? I'm using the new multistar guiding, will that make a difference?

In my case, binning the guide camera changes the scale ratio from 1:1.65 to 1:3.3

I'd guess it's a 2nd order effect. Try it without first (e.g. 1x1).

If you have issues, please post your setup and a log.

I don't think one could ever say "never" or "always" in this game. There are some good reasons for binning the guide camera. One is for noise reduction although one could also use downsampling/filtering in the guiding application if it is available. A large percentage of the practices in guiding applications are noise reduction (exposure times, binning, mean/median filters, hysteresis/aggressiveness). Another reason is to reduce the lag from when the guiding image is taken till the guide pulse is performed. This can be affected by in-camera processes, network time to transfer the image and time taken in the guiding software to process it. As with noise reduction there are many ways to address this including binning, bit depth, framing, network design and even where the guiding software runs in relation to the camera driver (same box vs over the network).
Binning 2x2 provides advantages for both noise reduction and latency so it is good general advice for someone starting out as it is simple to implement. In most cases it does no harm. The only issue could be if it makes the guiding scale too large compared to the imaging scale and even then it is unlikely to be a major problem as a starting point.

I bin my guide camera using an ASI290 mini in an OAG on my C8 f/7 at 1500 mm.

The pixel scale is less than 0.4"/pixel without binnning, and averaging makes the guide images nice and clean up to a gain of 400. I get way more guide stars this way.

With my 488 mm refractor, I don't bin.