Never tried it with other brands, but I actually mixed a kit of G.SKILL "Black Pi" DDR2-900's with a G.SKILL "PQ" set of DDR2-1000's. Of course, there was an overlap in the JEDEC data across the two kits for both latencies and voltage. This is not something I would recommend, even though the combination was rock-stable for as long as it was needed -- about five years.
If the manufacturer produces the same model (for instance, "-GBRL" or "-GBXL") with some slight difference in the design such as noted by the OP, there should be little doubt that they will work together.
On the observation concerning auto-configured command-rate, rseller's observations are no doubt accurate. I also had noticed that my motherboard would choose CR=1 on "Auto." But the memory spec as shown -- even in the mobo's XMP "Profile" -- was CR=2.
Without offering a guarantee, I'd suggest that the OP try upping the voltage for the IMC (if the processor is Intel). On chipsets and CPUs familiar to me, it was safe to set VCCIO as high as 1.2V, but you only needed to increase it from ~ 1.0 to around 1.13V to make the kits function with CR=1.