We also had a bit of a delay on our Leon but that was mainly due to the engine being discontinued after the order was placed – did get the correct spec / engine in the end but was a bit up in air at one point.
SEAT seem to do fixed trim levels rather than offer lots of options, if your willing to comprise on colour for example then the “same car” may be available from dealer stock.
Failing that there is normally a pretty decent range of similar sized estate cars on the scheme so if your not able to wait then there a good chance something else suitable will be available. Not sure on the current Advanced Payments but we previously had a Vauxhall Astra Sports Tourer in Elite trim and whilst not as “exciting” as the Leon was comfortable and very practical.