During charging there's ongoing negotation of power between phone and the source of power. After some seconds (of being plugged in), the final power is being set after such negotations.
This is required to be sure that both devices and also the cable are able to handle voltage properly. Ignoring unstable current basicly does what is says - it turns off negotiations and uses maximum power defined in both devices and cable itself, even if it's not stable.
In worst scenario, this can lead to the damage of a device, source of power or the cable. Usually it's safe to assume that everything is able to operate on defined max power, however as you know sammy cables are "faulty", and they negotiate lower voltage for a specific reason.
In short: In most common situations it should be safe to assume that everything is able to handle defined max power, HOWEVER nobody can assure you that you won't run into problems, negotiation exists for a very good reason to don't cause damage of any device, this is something like a "barrier", which isolates unstable things from stable ones and makes sure that nobody gets hurt. Turning it off may, or may not, cause problems, depending on various scenarios.
Galaxy S3: ArchiDroid 2.X | ArchiDroid 1.X | ArchiKernel | ArchiPort
Xperia M: ArchiDroid 2.X
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