In a komintern discussion that starts with text 299382, we came to the conclusion that files in .d-directories (xstartup.d, xlogout.d etc) that are not executable should probably not be run. The exception to this rule is files that are named <something>.sh, but they are not executed - they are sourced, so that's OK.
To confuse administrator's less, tl-run-xstartup.d et. al. should probably print a message with reason about ignored files.