You're thinking with a very American mindset!

T4 (Main) is geared up to handle any flights that are inter-schengen (i.e. imigration cleared) and also inside the customs area.

T4S (the Sattelite) is actually on two levels, upstairs is non-schengen and down stairs is schengen.

Although there are exceptions. [Non-schengen flights can be exit checked at the gate from T4 main, and the odd schengen flight goes from T4S(upstairs), etc. Lots of reasons.]

Rome is inside the Schengen area, and inside the customs area. As such it will likely go from T4(Main).

What drives things is the mix of their imigration status and customs status of the destination: e.g. parts of Spain itself are non-customs area (e.g. Canary islands), and parts of the customs area (e.g. the UK) are non-schengen.