Frasier lives in Boston in Cheers, so it'd be a continuation of the character's affect from there; Niles is introduced afterwards so may have gone for a consistency angle (or just shorthand for being snobs)

Martin would have been around for a while before settling down and having kids (his past isn't mentioned as much other than his time in Korea and career as a cop – in Cheers he's canonically dead), but also John Mahoney had a Mancunian accent in reality and faked an American accent once moving to the US so may have gone for "generic American"