Just a minor afterthought: You wrote about "the enemy ceding provinces occupied by your allies".
There is no problem if you, as the Overlord make a peacedeal, as long as the enemy country does have provincES to cede. Because provinces can be ceded to both enemy overlord or vassal in a peacedeal, once the overlord makes peace.
The problem you orignally mentioned only occurs if the enemy country has been, e.g. by prior wars reduced to have only 1 province left and would be forceannexed by losing it´s last province. Then your vassal is barred from making a seperate peace while you as the overlord are still at war and you, as the overlord can´t demand that your vassal forceannexes the country.
In a way that makes sense - while a lot of the BB points for annexing provinces can be heaped on your vassals back, the BB penalty for annexing the last province of a country and eradicating it from the map should somehow hit the one ultimately responsible for it.
wow, 2019 really does feel like ages ago.
Not saying using vassals to save annexation BB isn't a gamey strategy, but it's one of the most commonly used ones, and if the intention was to get rid of that trick, I would have expected to see it clearly stated in the patch notes. And then you have the historical reasons to allow vassals to annex other countries. Indeed, the whole reason some rulers accepted something ressembling vassal status was to receive the support of the larger empire against local enemies, whether external or internal. So for instance you have the Crimean Khanate who are a vassal of the Ottomans but eventually annex the Golden Horde.
Anyhow, even if you accept that change as desirable, you still have the problem of not being able to vassalise or annex the OPM yourself if your vassal occupied its capital. Instead you have to start another war, and get a head start over your vassal, and even that might not be enough if they have a higher ranking commander than you...
There should to be an option to get your vassal to sign the separate peace when they have a 100% against that other country (though that would create a problem when the occupied nation is itself someone else's vassal). Otherwise you should just be given control of that province as soon your vassal completes the siege.