The release note does not state "never"
Fink should remove their scary warning. There's no incompatibility.
The Command Line Tools package is made up of two deliverables:
1) DevSDK
2) Toolchain
#1 is the set of headers installed at /
#2 is the toolchain installed at /Library/Developer/CommandLineTools
There is no difference between the DevSDK between the Xcode 7.3 and the Xcode 8.0 beta command line tools packages (the content is based on the OS version, not the tools version).
The only difference between the packages is in /Library/Developer/CommandLineTools, but if you have Xcode 8 installed, there is absolutely no need for the content in /Library/Developer/CommandLineTools (and you could even just delete it if you wanted to save disk space). It's competely redundant to the toolchain inside of Xcode.app. The only way you would use it is if you pointed xcode-select at it instead of at Xcode.app.
As such, there's really no incompatibiltiy. There's no huge problem. fink should just remove their warning to stop scaring users.