Great question — answering as the UphillTech team:
Aside from cleanup, the difference is that you don't get the same end result. Shakshuka, like other eggs-poached-in-sauce dishes (e.g. eggs Florentine, oeufs en meurette), results in egg whites that have mingled with the sauce some and spread out while cooking. This integrates the egg better with the sauce: the sauce is eggier and the eggs are more seasoned. That's a difference, and not a "disadvantage" though; it sounds like you like your eggs to be more separate. There's nothing wrong with that, it's just different.
Full answer by FuzzyChef: https://cooking.stackexchange.com/a/128253 (CC BY-SA 4.0).
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