Yes, Map uses autocompilation for lists over a certain size and they will be packed if possible. The direct way would be

packed = Developer`ToPackedArray[unpacked];

myList is not a packed array and I guessFlatten therefore decides the result should be unpacked. Had the thing been packed to begin with there would be no unpacking by Flatten. Try it e.g. with

myList2 = RandomReal[1, {1000000, 10}];

As for Join, it is in fact seeing packed arrays since the component sublists of myList are packed. Ergo, a packed result.

Very interesting! I'm interested to know the cause of this. I sometimes also work with very big files...