Tips to "recreate" the spotweld look?

[69L48Z27]

Punching your holes in the top panel then getting your overlap correct and filling the hole with the mig is the optimal way.
Too little too late I suppose.
Can't really recommend a good looking way to help you, unfortunately.

^^^^^ This.
If you are grinding down your spot welds that means you blew too much wire in or you were cold. When you plug weld around the perimeter of the hole it will leave a slight indent. Using a TIG would give you more control. Overhead plug welding is pretty hard to do, at least for me. Those I have to grind.