It's not all of Mesopotamia, only a sliver or so in the North. Here's a map:Giving a branch of the Imperial family full autonomy over such rich lands still seems like a recipe for Civil War. But then again, they're right in the path of a Turkish invasion, very small window for any shenanigans.
This is the entire Empire, but you'll see that the amount of land between the rivers is not too large (of course there are extra bits on the other sides of the bank but not much). Full Mesopotamia would have never been on the table. That being said, the rest of the region is in total chaos-so maybe Kaisar Michael can expand quite bit southwards.
This is a recipe for civil war-but it won't be an immediate one for a couple of reasons. The Mesopotamians have no navy (and without that, bye Constantinople), the army is loyal to Basil II, Lord Komnenos (who has unprecedented power in the new government) and is not particularly against Basil III (the Egyptian forces are pro "little Basileus", rest benignly neutral) and Michael is seen as having gone native (to be fair he lasted the Dawd years only based on deep local support). So the Mesopotamians have no ghost of a chance of being top-dog in the near future: Michael knows this and so all wars he will wage will be against Mesopotamians and remaining Armenians. His eldest son is a hostage in Constantinople, and while he will soon have others from his new wife-they'll be seen as full Assyrians and will not advance his case at all, unlike his firstborn, who is still seen as Roman enough.
This does not mean Michael's heirs will not make a move against the Empire (if say, they have more of Mesopotamia under control to field a larger army), but the best they can do is East/Central Anatolia-Egypt and Syrian coast is a bridge too far with the current demographics and Imperial navy. Besides, the Turks are indeed coming soon.
Well, that did not quite stop Palaiologid civil wars (besides, they were effectively a corpse for there last fifty-maybe 100 years out of the 190 year run) which came with their own price tag. This duchy is a short term fix, but a bad idea long term.Could go both ways.A hereditary Macedonian duchy would mean that any potential non-Macedonian pretender would have to think twice before they try to usurp the throne.In my opinion,one of the major reasons why none of the other Roman Dynasties lasted as long as the Palaiologian Dynasty was that the Palaiologians were quite into giving out fiefs to family members.