It's not really any better a situation when applying for the partner-sponsored work visa than it is for the partner-sponsored residence, if you actually have to state you're
living apart, even for a good reason like work commitments.
However, could she be said to be living at home with you, and
lodging away during the week? Is she still getting some mail at your address, and is that where she is if she has a few days off? There have been times in my past when I periodically worked away from home, sometimes being at the other end of the country for more than a month, but if anyone asked me for my address, it never was anything but 'my house'.