I have modified ~/.xinitrc in the Xtc package to execute the scripts in ~/.X.d in order of the starting characters being numbers first, then letters. So if you want a script to run last, it could be named for example zzzsettime to run last, or aaasoundsetup to run first. Scripts starting with numbers will run before those starting with letters and will run in numerical order. This allows control of the executing order of ~/.X.d/ scripts.
~/.xinitrc is probably in your backup and would need to be removed from it to see this change upon update of Xtc.
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