Sorry! I was wrong! 
 
The file I mentioned ('kstars.kcfg') is produced before "make"ing 'KStars' and it's part of the source code. The file you found ('~/.config/kstarsrc') is effectivly the place where the settings are saved. You will find the guider settings under [Guide].

With my patch the [Guide]-Settings are the following:

[Guide]
AutoModeIterations=5
CalibrationPulseDuration=200
DECIntegralGain=35
DECMaximumPulse=500
DECMinimumPulse=50
DECProportionalGain=67
DECorrDisplayedOnGuideGraph=true
DefaultGuideCCD=CCD Simulator Guider
DefaultST4Driver=AOK Skywalker
DitherEnabled=true
DitherSettle=5
DitherThreshold=0
GuideBinSizeIndex=1 <- saved binning (new)
GuideExposure=5
GuideFilterFITSIndex=1 <- saved effect filter (new)
GuideScopeType=1
GuideSquareSizeIndex=3
GuidingRate=1
RACorrDisplayedOnGuideGraph=true
RAIntegralGain=35
RAMaximumPulse=500
RAMinimumPulse=50
RAProportionalGain=67
SaveGuideLog=false

Thank you for your work! Can you please submit an MR so we can merge this?

I see there are also [Capture]-settings and I can see the paths for local or remote saving, do you know off the top of your head if there could also just be a setting for which should be default? I feel like the default binning mode would be handled somewhere else though. Since I've seen the binning settings being stored in my 294MM config, they just don't seem to be used properly. I've downloaded the code but it was recommended to use some IDE which I don't have yet.

Storing of settings in KStars, EKOS and INDIlib has it own logic and is historically grown. ( I remember there was an entry in the forum regarding that subject, but I don't find it on the quick.)

As far as I understand the philosophy of EKOS, the settings related to capture images and NOT bound to the cam are saved in [Capture] . Therefore the binning of the cam is stored in the related XML-file (where indiserver is running), other settings (like 'CaptureDirectory', 'DefaultObserver', ...) are saved in 'kstarsrc' (where KStars is running). From both places they are transferred to the EKOS-module 'CCD'.

In EKOS-Module 'Guide' however things are a bit different: The settings used are saved predominantly under [Guide] regardless of the cam. (In fact there are a lot of cams which are multipurpose devices: Either they can be used for imaging or for guiding.) There is a very interesting point though: If you look at the CCDSimulator (starting with 'Simulators'-profile), in the 'INDI Control Panel' you can find a so called 'Guider Head", which follows your idea: In this place you can set actually some properties (e.g. binning) for the cam if used as guider! This settings override the ones in 'kstarsrc'. I don't know if there is a real camdriver implementing this feature. At least until now, I didn't find one.

I think I will submit a merge request for the patch I wrote. This way - I hope - saving of guider-binning and guider-effectfilter will emerge in 3.5.5.