I have read everything I can about this warning, but none of it corresponds to exactly my situation, hence this report.
I have a brand new Mac Mini M1, and a fresh MacPorts installation. This is not an upgrade--I have never had MacPorts on this machine, ever. I definitely have both Xcode 12.4 and the Command Line Tools that Xcode wanted to install. I do not know the version number of those tools because I don't know how to find that out. But it is whatever Apple provided by install a few days ago. I have provided all the incantations that I have seen on your web pages to install, verify install, accept licenses, etc. And this is Big Sur 11.1. Yet I see the following message when building various ports from source: Warning: The macOS 11.1 SDK does not appear to be installed. Ports may not build correctly. Reading other threads and guessing a little, maybe I am supposed to ignore the warning. If that is not the case, I sure do not know what I am supposed to do instead. I discovered this when I started to work on figuring out why the MacPorts py39.scipy port does not actually work, and maybe helping to fix it. (It fails scipy.test(), for example, or even segfaults if you "import scipy.signal" among other things.) I actually have a handle on the problem and would like to contribute a solution, but really first I would like there to be no uncertainty about whether I have a working MacPorts system itself. I am reporting this because I imagine that the developers would want to know if a brand-new installation on a brand-new computer does not actually work, or at the very least generates specious warnings. I know I would want to know that. I know that this is early days and ports themselves are expected to be broken for a while. But really I think MacPorts itself is supposed to install and work correctly on a fresh install on a new machine.