If a company get license to Workbench and other AmigaOS based application source code, is it possible to port Workbench and the applications to Linux 64bit or BSD 64bit?
In short: No.
Probably it would mean throwing away all the original code is it is AmigaOS dependant and relies on 32bit addressing (taglist, casting addresses to LONG, dos.library limitations). The whole AmigaOS API is limited to 32bit.
You'd be better off by rewriting the code from scratch.
You would not get binary compatibility anyway, so the questions arises: What's the point? Linux and BSD have tons of way better desktop and software already.