An integral part of my 'test track' layout is a yard ladder comprised of old 1970's era Atlas 2-rail switches with a Code 148 center rail added (same size as the running rails), and I've never had an instance of flanges hitting the ties. The back-to-back gauge of typical 3-rail flanges places them slightly inboard of the molded tie plates. Due to this I did have to remove the guard rails adjoining the frog to allow them to pass through, and also apply a thin layer of epoxy to the running rails where pickup rollers cross them, but this hasn't made them a source of derailments.
They can be seen in-use on my numerous 'test track: xxxx' videos on YouTube (same username as here), as most videos of trains starting from a standstill start out moving through one of said switches, (example below, one of the sidings using the modified track can be seen in the foreground of the opening shot, and the switch itself can be seen at 4:10).
I've run Lionel postwar/MPC/LTI, Williams, K-Line, Right-of-Way, RMT, Kusan, 3rd Rail, MTH, Weaver, Menards, modern and 1970's Atlas through them without issue, using track pins soldered to the Atlas joiners to adapt them to the 027 tubular that comprises the rest of the layout.
(slightly offtopic) These switches were recycled from my floor-layout days and were used since I built layouts that ran from room-to-room, hosting trains so long that they'd block walkways when parked, so I built lay-up yards to corral the consists when not running. The Atlas switches allowed me to pack more tracks together for increased storage in a given space, and more importantly, they were cheap (under $10 apiece for manual ones back in the early 1990's) and the place I got them from (The Red Caboose in Manhattan) also had the Code 148 rail and large-scale spikes I used to modify them for 3-rail use.
---PCJ