Yes it is true that the alternator will put out more to get a flat battery back up to the correct operating voltage. It would be good to verify your cables can still handle the extra amps. As you noted the danger is identified unfortunately by how warm the cables get. Mine are still in very good condition and did not get noticibly warmer the two times it has gone flat and been jumped. I say noticibly because you will always see that cable getting warmer than no load cables using a thermal camera (which i have). The cables are well capable of handling the extra load in good condition from my experience however mine is a southern truck with no green crusties in the wire(on this particular truck) my tundra on the other hand needs a new cable since it does have green crusties that were allowed to form by the previous owner in to the cable.
One additional thing you can do once starting an engine from a flat battery is to just let it idle for a while and not rev the engine to allow the alternator to give it full potential.
Also
@Photoman i believe did some testing with winching draws and the stock fusable link (and his upgraded alternator setup) and was able to get it hot but it took some considerable load if i remember correctly. I believe I am still fairly protected from overheating the wires by keeping the fusable link in play. I do have an extra link as a spare though.