Good point. How many channels makes a big difference. I am programming a new radio for when I travel, and manually putting in over 500 channels would take a long time. The software also makes it easy to organize your channels and update the radio with new frequencies. I have mine grouped by county and state and if I need to add a channel to a county all I need to do is insert a channel in the software and hit the send button. Without the software I would either have to put the frequency in a spare channel away from the others, or reprogram all the channels to get it in the same group.
Also, what mode or modes ? If you use a radio capable of multiple modes AM/FM/SSB/CW, etc. doing it by hand can be time consuming. It's other thing to have to program in addition to frequencies, tones, repeater shift, etc.
On the HTs (VX6 or VX8) Yaesu does not have delete memory function. You can hide the location or over-write it.
So... if you are like me and like to keep things ordered and by the numbers then the programing software is the best choice.
The application on the PC uses the cloning function of the radio. So every time you write to the radio it is a complete update of the radio memory based on the current data in the application and how it is organized.