You should be fine. I have pulled and installed several motors and transmission combinations in my wagon without ever trimming the lip. It just makes life a little easier during installation, and makes getting at the bolts easier if you ever pull separately.
YES it does!
I trimmed mine back for this very reason one time while the engine was out.
I too only went to the spot welds and I remember adding a few small welds at a few spots since I did not care about smoothing the firewall or anything.