Silly train ?? preferred reserved seats --

Milan to Florence I would have no preference as it is pretty much flatland to Bologna, then essentially one long tunnel to Florence. Florence to Rome also presents no major reason to prefer one side or the other.

I can't think of a reason on either of those trains to prefer one side to the other. Maybe if you are going in the morning from Florence to Rome and don't like sun on you sit on the west side of the train, the left side, or if you prefer sun on you sit on the east. If you are going in the afternoon you could switch it around....

It makes no difference how far forward or rear you sit, unlike flying, a shorter walk to your seat at Florence will mean a longer walk at Rome (both dead end stations) and vice versa. It really doesn't matter... It isn't like over the wings is safer...

If you are putting your luggage in the actual rack at the end of the carriage, by the doors, you might want to sit where you can see your luggage at all times; so near the end of the carriages.

As far as keeping an eye on luggage goes, the high speed trains make few stops, so luggage theft (or accidental grabbing the wrong bag) opportunities are few. Milano Centrale to Florence trains make at most 3 stops along the way, Milano Rogredo (shortly after you depart Centrale), Reggio Emilia, Bologna Centrale. For Florence to Rome Termini, just one stop at Rome Tiburtina, just before you arrive at Termini.

Nothing particularly interesting to see in either trip. Hopefully you'll have someone cool to talk to along the way, or just have something interesting to read.