The use of "Flowers of the Forest" in the lyric is because it is a mourning lament played over the dead of the battlefield.

Barnbrack actually have a version where they start with FotF and then go into NML.

I have a copy of the Furey's songbook where they credit their version with be learned "from the singing of.... (somebody whose name I forget)", which suggests they didn't worry about finding the correct lyrics before recording it.

Apparently there have been a number of attempts to identify if there was really a Willie McBride and sevral have been identified as having been in Irish or Scots regiments (no real surprise).

With regards to Irish nationalism, what really annoys me is when some ignorant sod (usually a Sun reader) tells me I'm singing a rebel song (presumably because it has a line about 1916 and was sung by an Irish band).