For example, have multiple star_flare_name, star_part_name in the textures>common folder, and have the drop down menus to select which one to use in game. Beats replacing them and restarting SE every time.
It would time consuming to integrate mod support for every texture in the program. Maybe this will be done someday, but not soon.
If you want to save a little time now, take some time and make some batch files that automatically copy and rename the files you want to use when you want to use them, so you don't have to do it manually anymore. This saves a lot of time if you're going to be switching between a lot of different textures frequently.
I had a friend of mine make a batch file template for me to use to do this sort of thing a long time ago:
set "source=F:\Program Files\SpaceEngine\textures\common"
ECHO | DEL *star_part.png*
copy star_part_HD.png star_part.png
::ECHO Y | DEL *star_part.png*
::copy /y star_part_HD.png star_part.png
In the above example, the currently active texture star_part.png is deleted, then another texture named star_part_HD.png is copied and named star_part.png. This makes star_part_HD.png the new active texture. You will need a batch file for each individual texture you might want to use, and none of the textures can be named star_part.png.