I would think the color from 16bit files are far better to superior at any ISO setting they will just give you the best possible image capture.
They're both still 16bit but it's a little unclear exactly what is different about the IIQ L file and the IIQ L 16bit files.
I suppose you might be right that once you push the ISO, any gains from the IIQ L 16bit format would be negated. But I've never seen a conclusive statement from Phase on this. Sounds like it is specifically designed to work with the 16bit capture of the IQ3 100 ...so maybe not using compromises the quality a little.
From Phase ... "Why IIQ L 16bit?
Both IIQ L and IIQ S are 16bit le formats when using CCD digital backs (IQ3 80MP/60MP, IQ280/260, IQ180/160/140).
... The IQ3 100MP features a new and Improved CMOS le format “IIQ L 16bit”. The IIQ L 16bit is, similar to the IIQ L, a completely lossless le format. It handles output in full 16bit from the IQ3 100MP CMOS sensor which is a new feature introduced with this special CMOS sensor.
While IIQ L 16bit provides the ultimate quality possible from the IQ3 100MP, the file size is also larger and the capture rate slower when compared with the IIQ L or IIQ S."