I'm in Ecuador right now, returning to Peru. Also traveled in Mexico and Guatemala:

Inside parking with a locked gate is very preferable. Not sure what size moto you are traveling with, but bigger will be harder to find more creative secure parking for the night. Last night I rolled my 250cc moto across the entry of a motel and in to a dead end hallway. I've had creative places for parking now and then that would not be possible with bigger moto. Just ask at your lodging for parking. There are also gated and manned public parking lots in some towns. Inside a secure area is what you want for the night. After that, don't worry about it and enjoy your evening.

I have a 250cc local moto, vs an exotic that is not seen in SA. Less of a target. If you have an exotic moto, you'll have to learn as you go. I will guess that the exotic moto moreso identifies you as a richer gringo vs a moto to steal. What is a thief going to do with an exotic moto to part out or sell?

I always bring all my soft luggage in to my room for the night. I don't have any cases or hard luggage. I like the lighter weight of soft luggage. Light weight moto is very preferable for my travels.

During the day I keep an eye on the moto, and lock the fork with the ignition lock. When eating some where, I try and have a view of the moto. Sometimes I cable the moto to a secure post. Soft luggage; I just trust in hope and luck and park in a secure place. Stopped to see something, I often ask about safe parking. I have my bag wrapped with a cable so it is more difficult to remove. I have a backpack instead of a tank bag, so I carry the important stuff there and it comes with me. Never had troubles with my soft luggage. I tend to cross borders less busy, so haven't had border troubles.

I had a fellow looking at my sheepskin one time while I was eating at a road side stand. I just went over there and asked him what he was doing. He said he was trying to figure out if it was sheep or lama... Who knows his intention? No other issues experienced other than that one minor incident.

Just be prudent, but don't sweat the security.