OK, here's some more info on this. The Options settings control all of the searchs: incremental, command line, along with the Find and Replace dialog
The options in Tools > Options > Search are used the in the following places:
a) The very first time the Search Options dialog pops, after that, dialog history takes over, unless:
i) You set the Tools > Options > Search > Tool window option > Initialize with default options setting to True, then the options are reset to default every time it is brought up, or
ii) You use the right-click context menu in the Find window to Use default options to reset to the defaults state.
b) The default options are always applied when using Quick Search/Quick Replace command
c) The default options are always applied when using Incremental Search command.
d) The default options are applied to command-line searches (/ command) if you don’t specify options explicitly.
e) The default options are applied to Selective Display commands when searching by text.
So we don't think most people would like it if the values set in the Find and Replace dialog changed how the others behaved. We're certainly open to feedback on how to make this more manageable.