Trucks that can accommodate 3 rail wheels have wide bolsters resulting in the side frames being closer to the outer edge of the car body than trucks designed for 2 rail wheels. If you retain the 3 rail trucks and just replace the wheels with 2 rail ones (I find .045 wheels to be a good compromise between looks and reliable operation) you've addressed the operational issue but not mitigated the appearance one. (admittedly I'm ignoring P48 gauge trucks). One option to consider is selling the 3 rail trucks and installing 2 rail ones. My go to replacement for Bettendorf freight trucks has been Intermountain trucks and wheel sets (they require minor assembly). They look and operate well, and can be found for under $10/pair.
The appearance issue is very subjective. You might try re-wheeling one car with 3 rail design trucks and putting 2 rail trucks under a similar car. Compare the appearance and see if the difference matters to you.
