Great progress! Yes, if you are setting up "fresh" every night you want to be making sure that you are eliminating every variable going into the alignment process - this is one reason I moved to a permanent setup!
I had a quick look at the driver notes for the 8300 you're using and saw "Hardware binning (vertical only. horizontal binning is implemented in software)" - not sure what this means in terms of the difference between teh alignment and imaging modules, but might explain what you're seeing. You might want to try playing with the binning in the driver control panel. IO'll do some more reading and see if I can find any pointers.
My advice, for the money, getting a ZWO even just for PA would be a huge headache saver - you're there to enjoy your hobby, not bash your head against a hardware designers bad choices.
For me, after a lot fo messing around I've found the tricks for hassle-free alignment can be to;
1). (oddly) align the telescope before darkness - this takes a bunch of hassle out of the process later so that you are fine tuning versus major moves
- level and stables your tripod, mount and scope - mark the legs, etc to speed this up - keep the process as close to the same between nights as you can
- do a "starless" polar alignment - the simplest way I have found for doing this is to use my iPhone to get the scope RA axis to the same angle as my latitude (within the degree of accuracy that the iPhone level allows), if you can get better using something else go for it.
- likewise use the compass to point towards either north or better still the NCP
- while you're at it, make sure all cable drag etc is addressed, scope balanced - these things matter
2). be REALLY clear about where the mount is getting its location from
- as mentioned, DISABLE Site Info, it's not intended for local operations
- check the INDI control panel - is the mount time and location being "reset" by kstars?
- I know with my LX90 that the mount had to be the time and location "master", if kstars or a GPS tried to update it, it would throw off tracking and all manner of things, so my advice is be conservative until you can be sure how your mount and INDI interact (read lots of blogs!)
- see control panel screen shot for what I am talking about - you want "Mount updates kstars"
- do this before connecting your mount to the computer
3). after dark, reset the mount and EKOS to a known "parked" state
- align to the NCP with an eyepiece the best you can, again save time later
- park the mount (weight down, scope pointing to where you think the NCP is)
- reboot/restart everything - mount, computer, INDI, etc - but do not plug INDI in yet
- if you are using the mount as time/loc master, then do the basic alignment from your mount manufacturer (1 star should do for now, 2 better)
- plug in the mount and fire up kstars/INDI
4). start the PA tool with 30' increments just as you did originally
- a 30 second refresh is a long time, assuming this can't be addressed, then my advice is to get as close as you can but an arc minute or two out should be considered a huge success under the circumstances, hence the ZWO
- note that if your alignment is getting worse between runs, do the opposite of what the tool tells you to do, it's a known "strangeness" (hard to say it's a bug as it's not easily replicated between sites)
5). repeat 2-3 times until you're satisfied (or forever if OCD over 20 arcseconds drives you crazy)
- then ideally run out an buy a Telegizmos 365 cover and leave everything in the yard
6). enjoy imaging instead of tinkering
As a side-note I am thinking of adding a second-hand AVX as my portable mount, so I might be able to add some real-world experience to this thread soon.