Sure you can. Pass validity is not defined via cities but via the railways companies. You can use any train of the participating companies.

If you have a flexipass though and only travel a short distance, do check normal fares to see if it's worth to use a travel day for your journey.

In general, yes, if you have a continuous pass then this is a great way to travel in and out of cities. Bear in mind that in most cities you can’t use your pass on local transport like metro/ tram or bus. And often you will want to make some journeys on local transport, so you might end up buying a day-ticket anyway.

I’m not sure which trains between Rome and Ostia are included in the pass. I would guess again that the commuter train is OK, but metros aren't.

Come to think of it, the line to Ostia is not included in the pass, since it is not operated by a participating company.

do you have any recommendations of cities that have access to a railing system that is included in the pass ?

The S-bahn is included in German and Swiss cities, as well as Vienna and Innsbruck.

This is commuter rail with several stops in the city. You won’t have access to the whole city transport, so it won’t get you as close to your destination as the metro would.

In Brussels, you can use the pass to get between, say, Brussels South/ Central/ North.

Hi, just a suggestion.   When you are planning your route, if you want to find the smaller towns on your planner, put in your required destination, click on no seat reservations.  This will bring up the route and changes of trains, but for each part of the journey you can open it up further to find all the stations that the train stops at, and you can get on and off as you like with no additional costs.  A great way to explore away from the cities, and also a good way to find cheaper accommodation with just a short journey to the more expensive destinations. 

And recommendations for Italy ?

In Italy also commuter trains are included, that are run by Trenitalia, Trenord or Trenitalia TPER.