Its preferred that styling for everything but the editing window be done with GTK CSS. I'm no expert, but I believe it can specify differing settings from states like focussed etc. Not sure about transparency, but maybe opacity will work. Probably best to read the GTK docs/tutorials etc and try it.
For selector purposes both the Find dialog and the Replace dialog are called "GeanyDialogSearch", not sure how well that will work, but may be ok if only one of them is visible at a time. Otherwise we can probably change one if needed.