If you compile a program on FreeBSD, no you can't copy the executable and run it under Linux (or Windows).
However you can copy the source to Linux and compile under Linux. That executable will only run on Linux.
Provided you are using standard stuff, the libraries and headers are named the same, no change to code is needed. Ditto for windows.
So absolutely yes, you can develop on Linux, then when you are happy, copy the source over to FreeBSD and compile it there.