Instead of making a huge text, here are the basic complains and problems I face all in one picture.
If anyone has an answer to my questions, or thinks I’m wrong about something, I’ll be more than happy to learn or discus. 
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Use OrcaSlicer. Put your PA setting in the filament User Preset where it belongs. OrcaSlicer will put that value in the g-code sent to the printer and override whatever PA setting is shown on the Device tab. Even though Studio does not display PA in the filament settings, if you let your presets sync through the Bambu cloud, Studio will also use the PA setting from the preset instead of the value stored on the printer/AMS.
I think (could be wrong) that Bambu stores PA settings on the printer to facilitate printing direct from MakerWorld, with the rest of the slicing being done by their servers. If you do your own slicing, and have your PA value in the preset, there is no need to have PA values on the Device tab.
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Regarding your last but not least: I often work on models in Bambu studio that I will not print with the current colors in the AMS. I don’t think I should be limited to only the colors in the AMS when I work on a model in Bambu Studio.
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I in the past saved my profiles via Orca-Slicer, but its a bummer and shouldn’t be like that. I though maybe I’m missing something, but apparently not 
I might open a case on Github in hope they do something about this, or at least explain the “why”. There’re just so many “why’s” here… XD
I get your point… The preview makes it easy to see how a model would look like in different colors. That’s true and something I did not have in mind. 
One thing that really bugs me is that after I calibrate the pressure advance for a filament and get it working where I can select it from Bambu Studio and also from the Printer then two days later for some reason the profile for that filaments pressure advance does not exist any more.
I just put the pressure advance setting in the filament Start G-code after calibration and ignore the separate K value profile because it will just disappear anyway.
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G-code… That is something I hadn’t thought of.
But now I’m curious… where did you previously save the PA settings? Is there another place apart from k-factor in AMS setting?
After calibration provides the k value I use that value in the G-code.
I Open Filament settings for the filament I want to update, I go to the advanced tab and add the following line to the end of the Filament start G-code section:
M900 k0.20 ;set k-Value Pressure Advance
Change 0.20 to the k value per calibration of the filament.
To verify it’s working, slice a model with just that filament and review the first layer G-code with the horizontal slider, For generic PLA, I found the k value being set at line 1068.