Hand taps have straight flutes with no special geometry to force the chips (in ductile materials) to curl in a controlled direction. Thus, they tend to plug themselves with chips if they are run several turns into the hole.
Yes, you can tap a hole by hand with a machine tap, but the need for some sort of guidance system is mandatory, because they typically have fewer flutes and are less stable to get started exactly straight into the hole. Mind you, hand taps are also better used with a guidance system too, however, with the long taper of a 'taper' tap, you can usually get the tap started and square it up by pushing this way or that way as you start it, and checking with a square.
A bottoming tap is really only meant to clean up the last few partial threads left by a plug tap. I cannot imagine using the bottoming tap to tap an entire thread, as the cutting force is very high. If you have to tap that close to the bottom of a blind hole, use a spiral flute tap, as these have maybe only 3 threads of chamfer. Then hand tap to the bottom with a bottoming tap if you must.
