>I'm not sure whether there is smart solution for this matter.

Maybe there should be an "auto" folder at every .tex file location instead
of only in the master location, I imagine this could solve a few of the
issues. The path to the .el file would have to be constructed using
"../", then the path to the included file, then "auto/" and finally the
filename. In my example, the paths to the .el files in the master's .el
file would end up as follows:

"../auto/preamble0",
"../auto/prea mble1"
"../../../auto/preamble2"
"../auto/preamble3"
"../folder/auto/preamble4"
"../../auto/preamble5"