I speak as someone who did the NPPL (SSEP) when it was first introduced, mainly as it was a little cheaper. The standard in respect of the NST and GST are exactly the same, so I don't think safety is an issue here.
I then upgraded to a JAR PPL which proved to me something of a headache. E.g. the QXC for a NPPL only needs to be 100nm compared to 150nm. Guess what, mine was 120nm so I had to do another for the PPL! Despite having flown all over the south of England with the NPPL!
No issue with groundschool - same 7 exams. (Microlights you do need to do additional exams, can't recall which ones).
But... the biggest issue is that NPPL Ltd who administer the NPPL licensing and the CAA do not communicate terribly well in my experience. The CAA had no record of my groundshool passes. They accepted I had an NPPL and that I must have passed the exams to get it, but they wouldn't issue the JAR PPL as I couldn't provide evidence of the groundschool passes! Fortunately a very helpful lady at NPPL e-mailed me the scanned copy of my groundschool records which I was able to supply to the CAA and all was well.
My advice; unless medical issues prevent it do the PPL from the outset unless you are cast iron sure you will never want an IMC, night, MEP etc... Unless you achieve the NPPL in minimum hours the savings are unlikely to be that much.