I always check my applique pieces with my overlay before I trim away fabric. I never trim blindly.
When I can, I wait to trim away excess fabric. These photos show a good example of that... You can see that I have sewn down the side of the stem with the leaves. Before sewing the 2nd side of the stem, I lift the stem up and trim the end of the leaves even with the stem's turned-under seam allowance.
The longer seam allowance makes it easier to pin the stem firmly in place over the leaf. If the end of the leaf is not pinned down you have to be really careful when you sew, not to let the leaf "wander" out of position.