Yes, these warnings are really annoying and to my mind not needed at all!
To get rid of these warnings you have to edit Innovator/Client/javascript/search_container.js:
Just set bSwitchToNewSearchMode to true and remove/comment the aras.confirm() call in line 584:
[embed:dc8ab71f-3b98-42d9-b0f6-e21e02a0f8e2:49c6e09e-50a3-4723-87f8-217851b8b5bc:type=javascript&text=const%20bSwitchToNewSearchMode%20%3D%20true%3B%0D%0A%09%09%2F%2Aaras.confirm%28%0D%0A%09%09%09aras.getResource%28%0D%0A%09%09%09%09%27%27%2C%0D%0A%09%09%09%09%27search_container.aml_is_not_compatible_with_new_search_mode2%27%2C%0D%0A%09%09%09%09curModeLabel%2C%0D%0A%09%09%09%09newModeLabel%0D%0A%09%09%09%29%0D%0A%09%09%29%3B%2A%2F]
