Setting up multiple O365 organisation accounts on iOS
Going off the title question - Setting up multiple O365 organisation accounts on iOS and interpreting that to mean you want to have multiple Intune profiles on a single iOS device because you (or your customer) has multiple accounts managed by different Intune servers; unfortunately, the answer is no, this cannot be done.


  Intune only supports deploying app protection policies to only one user account per device.


Microsoft details this in their support document What to expect when your iOS app is managed by app protection policies.


  Read the following example scenario to learn how Intune handles
  multiple user accounts.
  
  User A works for two companies: Company X, and Company Y. User A has a
  work account for each company, and both use Intune to deploy app
  protection policies. Company X deploys app protection policies before
  Company Y. The account associated with Company X will get the app
  protection policy, but not the account associated with Company Y. To
  have the Company Y user account managed by the app protection
  policies, User A must remove the Company X user account.