I don't understand you at all.
The "mark all" keybinding does not follow the options set in the find dialog box
but it makes the same as "Find -> Mark".
The options for the "mark all" keybinding could be set in the preferences dialog separate from the search dialog.
Really? How to do this? In geany 1.30 it is the same functionality, it doesn't work separatelly.
If to do as I request it will be two different functions, as for me - Mark All very usefull. And now I have to use Find with preferences, but it can be done a little easy.