KDE 6 seems to have gotten rid of run command, mark taskbar entry and log to a file options in applications specific settings under notification settings, only play a sound and show message in popup actions remain.
Are there any plans to bring back this functionality in future updates?
There is an open bug report for it. Seems like it might be brought back from what I have read on there. https://bugs.kde.org/show_bug.cgi?id=481069. Someone has commented having already re-implemented the feature, but they seem to be stuck on something. If you can perhaps consider helping them out.
Thats great news thanks for letting me know!