Can build engine be created from command line?

No, the JBE has no option to create a build engine. This is a on-time effort to be done in the Eclipse client. It would be possible to create a Plain Java Client Library application that creates the build engines. If you don't have to create hundreds of build engine ID's which would require the same amount of processes, I don't think it would be worth the time. It would however be reasonably easy to find the code in the Eclipse client.

You have to develop a script using Plain API in order to do it by command.