Gilmour has developed a very nice intonation and a great Stratocaster tone. OK he plays very clean, sometimes too clean not a Hendrix, SRV or Blackmore sound which are awesome in their own. Clapton´s Stratocaster sound is not my cup of tea, somehow thinnish without the right pressure. I liked him more playing Gibsons like the SG in his Cream era or the Beano Lespaul.
Not that I prefer one instrument over the other but it seems the Stratocaster does not fit Clapton's play - only my personal view and to each his own.