So this “new way” mainly concerns the OSMC remote controls. If you don’t have a dongle for one of those remotes plugged in this new custom keymap is not loaded. If you use a keyboard, or another remote or controller that presents itself to Kodi as a keyboard then there may be some interaction which you can mitigate by turning off the custom map as outlined [here].
If you have existing keymaps your using in your userdata folder (including what is created by the Keymap Editor add-on) these are not deleted, modified, or disabled. Any existing keymaps are actually loaded after our new custom map so your tweaks will not only stay in place, they will also affect the OSMC remote as well.