systemd doesn't change anything here. There's no reason to avoid it. systemd itself will work fine if /usr is separate. However, a lot of stuff that we ship by default on most Linux distributions these days won't. We just warn about that *fact*.
So, let me repeat this and make this clear:
A) systemd itself works fine with seperate /usr
B) if you want to fix this, then fix the specific programs, which are not systemd
C) this is a statement of fact, on the status quo. It is not a change in any way. It isn't news in any way.
D) this is just a warning. You may ignore it if you wish.