If there are differences between the macOS and Windows versions of the keyboard layout of the majority language, you should keep those differences also in the layout for the minority language. The idea is that we stay within the tradition and specifications of each platform, and we try to make the differences as small and as systematic as possible. This should make for the best user experience.
For most of the languages in the Giella infrastructure, there is no predefined locale within Windows. You can create one yourself to go along with the keyboard layout, like this example from Võro:
targets: win: locale: vro-Latn languageName: Võro kiil
This will make it possible to install spellers, and tie the speller to the keyboard language, so that MS Office and other applications in Windows will automatically use the correct speller when switching keyboards.
You should consider adding a separate Cmd-key layer, to make the command key behave identically to the majority language layout. If not, the command key will be tied to the actual letters produced when pressing the relevant keys, which will not always be what the users expect. Example: