Kale, you are correct that you are going to get the same plant if you take cuttings and root them.* If you collect seed there is the risk of cross pollination.* If you only have that particular rose in your garden, and there aren't other roses nearby that insects could bring pollen from, then you might get the same rose.
With heirloom tomatoes it's the same.* You shouldn't grow other varieties of tomato near them.* With tomatoes the wind can help pollinate the flowers, so you can shake the plant for that and don't need the insects as much.
When weeding, the best way to make sure you are removing a weed and not a valuable plant is to pull on it. If it comes out of the ground easily, it is a valuable plant.