it looks like LimeSuite is packing 2 12bit samples into 3 bytes therefore the actual rate on the USB link reads as 3 times the Lime sample rate (on the host side before/after hardware interpolation/decimation).
I agree with your analysis (three bytes per sample) and 4Mhz sample rate gives 12MB/sec data flow, but less than 4Mhz gives a fixed 2.043MB/s flow which, at three bytes per sample, would be 681kHz sampling rather than 3.9MHz sampling. That is the part that is curious.