A long rod crank requires pistons that have the pins moved also to account for the longer rod. In wiesco long rod pistons are 795 series, not sure about Vertex because no one besides vertex would recommend running them 😁.
Spacer plates are, as you said, to avoid having to cut the domes. They also set the lower port to the correct location but make the upper port timings worse. Not to mention the possibility of air leaks. If you want to get proper performance from the engine send the cylinders to get ported for the 4mil crank, buy cut domes, and throw the spacer plate in the garbage.