Well I am not too familiar with Toyota parts prices, but you should generally try and get the best parts available. Dealership will always be more expense as compared to open market, even for the same quality parts.
Not necessary to flush ATF but, personally I won't like my ATF being drained in dirty pans and then kept in the open for many hours while the axle is being repaired. Hence, personally I would always like to put in new ATF.
ATF has no link with axle seal leakage.