B4: The Lost City is a classic module for D&D. At one point it (in)famously stops giving full description of the rooms but instead lists monsters in each area and tells the DM to figure out why they're here themselves. Once the reprint will show up in new anthology, I'm sure people who complain online whenever WotC uses "ruling not rules" or "DM decides" or "these parts were left for the DM to fill in" in their design (and then continues buying WotC books to keep bitching and doesn't touch 3rd party or other games for some reason) is going to be normal about it. /s
They could make a program where you give it the players' character sheets and the encounter and it simulates a bunch of battles to see how they do. But failing that, you could make CR be a good average, where you could just look at that and adjust based on what the strengths and weaknesses are. I haven't actually played 5e so I don't know this from personal experience, but my impression is that they haven't done that. Some creatures just don't have a CR that matches them in general.
There's also no system for figuring out the CR of an encounter with an arbitrary set of monsters and enemies with class levels.