I mean you're just describing make but with hashes instead of file modification times. It's probably the most common criticism of make that its database is the filesystem. If file modification times aren't meaningful to your workflow then of course make won't meet your needs. But saying the solution is 'make with a different back-end' seems a little silly, not because it's not useful, but because they're not really that different.

GNU make handles multiple outputs alright but I will admit they if you want something portable it's pretty hairy.