Sure, that's a good point. I'm more concerned about system breakages, where - say, for example, you remove Messages because you use an OSS alternative, and suddenly the Phone app stops working correctly because the Samsung developers tied then together somehow.

"Safe" in this case means: "will my system still function if I remove this app and use an F-Droid app instead." The answer isn't always yes; my example of the Phone and Messages app is real on my Samsung device. Regardless of my settings, the Samsung Phone app keeps trying to open Samsung's Messages, and I'm afraid removing it will break the Phone.