WL#1119: Support using different compile options for embedded server

The embedded server should be able to be compiled with seperate options from the
actual server.
Example:
We should be able to compile the server with Innodb support, but the embedded
server should be able to be compiled without it at the same time.
Same should go for all options.

If this a large amount of work we can push it into 5.X, but we really do need to
make this happen if we are going to push the embedded server into usage.