Either Iso are selling at a low margin, or something about the Rega version is better necessitating a higher price. Rega have claimed that one of the main factors in the cost of the RB1000 is manufacture time. This is higher than for other Rega arms because the tolerance levels for the base parts, bearings and adjustment are tighter.
Perhaps Iso and other 3rd parties get a lower tolerance version which can be offered at a lower cost.
You'll really have to ask Rega and trust their answer.
You could try asking Rega's Paul Darwin who posts here occasionally.
To the OP, there isn't going to be an answer since I seriously doubt you'll find anyone who has reliably compared those on the same P9. The differences are going to be very small indeed where the same cartridge is used.
In this position I would stick with the RB900. Were the newer arm a fundamentally different design then I might consider a change. But it isn't - its a small variation to an already fine arm.
If however, the cost is irrelevant then just buy the RB1000 because it looks a bit better, is better made around the base and on balance won't be any worse
