You can still get alliances as a Hegemon, it's just harder. The only nations you're outright blocked from forming as a Hegemon are other Hegemons, and I have only once seen the AI claim Hegemony.
This is a similar problem to Savoy's mission to have an alliance with France who must have 150% army strength compared to you. Fine if you start as Savoy, ridiculous if you start as say Montferrat, where due to your starting position you can have the economy to field the largest army in Europe bar the Ottomans by Adm. 10 (where you can form Sardinia-Piedmont and inherit Savoys missions). There are no doubt other such missions too - edge cases not designed around completing them in the very late game, or when you have expanded way past where the game expects you to be when you get the missions. Like a German minor already being in position to claim Hegemony without having first formed Germany.