This is not an exhaustive list but, the original Leon sans bodykit was launched in the UK about 2000, bodykit added to Cupra version for 2003 model year, which was kept for the FR when it replaced the cupra (titanium mirrors added plus different wheels and some interior changes).
Cupra R launched somewhere around 2002, continued largely unchanged (visually) until production ended last year.
End of line FR models (late 2005, or FR+ as they seem to have been dubbed) featured all sorts of odds and ends. The 1.8T got Cupra R 17'' alloys but kept the old Cupra style bodykit. The Diesel model gained the full R bodykit and 17'' Cupra R wheels, plus revised rear badging. In the change over period before the LCR add ons there seem to be all sorts of specs where SEAT were probably clearing the decks of parts before they changed all the tooling and orders from their outside suppiers.
From memory the 'Cupra' bodykit first appeared in non UK markets on the 2.8 V6 Leon Cupra4 just to add to your confusion.