It WILL make a difference if there is a chance to damage your system each time you plug it in and out - Doing any other way would involve an extra swap, and twice as much chance that you bend or mess up the cable - It is good advice. Not to mention, if you are having intermittent issues while installing drivers for the hardware that is having intermittent issues? Ya, not good at all. That would be similar to OC'ing your machine until the point it is NOT stable, and then trying to do a bunch of Windows Updates or other system-OS intensive things, and then being surprised that all your data is getting corrupted.
I have seen a LOT of benchmarks showing higher scores with the riser\extension cable (when it is working 100%) - Not sure how that is possible, but it is happening and it is definitely not impossible. Its all little micro-differences, so each test will vary, but I was surprised to see a few HIGHER with the cable (even by a few points, #### it SHOULD be lower!)
http://www.overclock.net/t/1427731/pci-express-extender-cables-benchmarked