A tower cooler, in a tower case, is sitting in line with airflow from the intake fans. Some portion of its intake is going to be directly from that stream.
In contrast, a top-mounted radiator (I assume we're talking about like a 360 mm) is going to have 3 fans. That's probably more than doubling your number of exhaust fans and they'll be drawing air from wherever they can get it, including the GPU-heated air. So, if we hold the number of intake and dedicated exhaust fans constant (or replace some of the exhaust fans with the radiator), you just end up with a more heavily negative-pressure setup that will tend to pull air up from the GPU more.
It's very hard to argue hypotheticals, without going into specifics of different airflow setups, but I think
@TheHerald has a point - and one backed up by personal experience. I'm not saying you can't do things to try and improve either configuration, but I think simply switching between a tower cooler and a top-mounted radiator, without changing anything else, will tend to work out as described.