Most every engine I've ever seen has swedged superheater flues. From the sound of things, the swedged end were about 1 inch too big to fit into the flue sheet, so they were reswedged down another inch. The amount of heating surface lost in doing this isnt even worth measuring. The big reason behind swedging is to get good water circulation around read flue sheet, which is likely the 2nd hottest spot on a boiler. The tightly packed tubes would otherwise restrict the circulation, and allow the sheet to heat up more then it should, which could cause leaking tubes or maybe even a warped sheet.
I know of an engine without swedged flues, so I guess we will see how that goes. I don't think its the end of the world to either swedge or not, but the ancients did things for a reason. Ed made the right call reswedging the flues rather then opening up the holes in the sheet. Boiler work is a pain. and having to redo a thing or two is pretty normal.