I do not know anything about the Wilson build kit, But I do have a factory Wilson 458 SOCOM, and bought one of their 5.56 uppers for it as well.
The rifle functions perfectly with both uppers. The whole concept of the 458 SOCOM, was that it would work with a standard 223/5.56 lower, with NO changes.
You are correct the ejection port must be opened up a little wider, from what I have read, you must be careful not to remove much metal from the tip of the port, if you do the trap door will not remain closed. most of the material is removed from the bottom of the ejection port.