Most stuff compiles cleanly on the new Apple Silicon/M1x processors without drama, (invoking compiler-type arm64).
I now recommend using Homebrew rather than Fink, primarily because Homebrew is far more up-to-date, and runs natively on M1 processors and on Intel processors (automatically picking the right one for your computer), whereas fink (currently) relies on Rosetta2 as an adapter. Also, you can install native versions of Coot and PyMOL and many other open-source software packages that structural molecular biologists favor. In addition, Homebrew will install an X11-independent version of the software whenever possible.
If you have intel-compiled command-line software (like the current CCP4 suite), it can still be used with Rosetta2. The key to doing this is to start up a new unix shell like this:
env /usr/bin/arch -x86_64 /bin/zsh --loginAlthough zsh is the new default shell (as it should have always been), you can use bash or tcsh or whatever suits you. Everything you do within that shell session will be within an intel-emulated environment. Everything I have tried so far simply works without issue.