I didn't have any interference issues with the new added parts so I thought I could avoid trimming the spar flanges. I learned from Van's support that the reason for the flange trim (and removal of one rivet location) was to direct the loads into the new strengthened spar.
So I trimmed the 4 locations using a dremel while using the provided stainless steel sheet to protect the spar and skin. After deburring they were primed with all the other parts.