BEWS12.5 does support partitioning of an autoloader, so you can carve up your slots and assign them to jobs.
However, to my knowledge, BEWS doesn't support the sharing of an autoloader with another application. You could install both on the same server, but would have to disable/stop the services of 1 while working with the other. Same sort of concept as Removeable Storage Server really...that needs to be disabled otherwise BE doesn't run correctly/at all.