Will xtrabackup compiled against Percona-Server work with standard mysql-server?

General question. If I compile xtrabackup against the Percona-Server source code base, will that same binary be usable with a standard mysql server 5.1 setup with the innodb plugin?

Yes. But don’t compile it yourself. Use the precompiled binaries. It makes it a lot easier to determine where the problem is, should you experience any troubles, if we don’t have to guess that you compiled something wrong. Also, the xtrabackup source code is not designed to compile against all versions of MySQL source code, only specific versions (although the resulting binary will work on more than just that version).