You'd be surprised at how low of an acceleration is required for propellant settling and transfer. On the order of 0.0001-0.01m/s^2. At a 310s Isp for the ullage thruster, that's between 0.01kg and 1kg of propellant usage per second. Even if it takes an hour to transfer fuel (on the ground, fuel is transfered in about 20 minutes and in flight, all the propellant is transfered from the tanks to the engines in ~8 minutes), we're only talking about maybe 1% of the propellant needing to be used for ullage thrust and perhaps as low as 0.01%.
ULA has published a paper on the topic: https://www.ulalaunch.com/docs/default-source/extended-durat...
If they were so inclined they cold even recover the helium from the tanks they are filling and use that to assist with pumping pressure.
SpaceX has done experiments with how much thrust is necessary for ensuring propellant settling. That's one reason you often see a video feed of inside the upper stage liquid oxygen tank during a Falcon 9 mission. It doesn't take much thrust to ensure propellant settling. Not at all an open question.
This always struck me as one of the least questionable new things in SpaceX's architecture. Much less Kerbal than most Mars architectures which require assembling a massive craft in LEO or whatever.
(One would be remiss to not mention the history of refueling... SpaceX's competitor ULA had been pushing refueling and orbital depots, which it called "distributed launch", since its formation, but has only been able to do small experiments since one of its parent companies, Boeing, sees orbital refueling as a threat to NASA's SLS rocket, which Boeing is the main contractor for. That's a huge reason for a lot of the "skepticism" about orbital refueling you sometimes see in aerospace circles, besides the usual pathologically conservative mindset of many grey beards...)