Hello @Jonathan Berg,
To streamline the process of MFA in mobile devices it is advised to use Modern Authentication as it works better with MFA and CA policies. Migrating from ADFS to Entra ID Authentication will also help in utilizing Conditional Access policies natively. It is also recommended to utilize Outlook mobile instead of the native iOS/Android mail app. Outlook supports modern auth and conditional access policies better than native apps this would help avoiding the dual prompts.
For the second part as your domain is federated with ADFS, the authentication is redirected to ADFS by default. Microsoft 365 uses domain federation settings to determine whether to use ADFS or Entra ID. It would not be possible to selectively divert the redirection for mobile phones or some services. It can be considered to move towards Managed environment where the authentication will be handled by Entra ID and removes ADFS dependency.
Seamless SSO only works for domain-joined Windows clients on corporate networks (via Kerberos), so mobile devices won’t benefit from Seamless SSO directly. To achieve slightly better experience on mobile phone you can use Device enrollment and compliance policies in Intune and combine with Conditional access policies. Moving towards modern auth and device policies will help achieve seamless like experience on mobile phones as MFA prompts will be minimum and refresh tokens would be used for future logins.