The same issue was brought up in my game as I have a player that wants to play a shapeshifting druid. I have not been able to find a answer to this question anywhere.
I do not think that it is logical myself. I have an idea as to why they might do it this way though. This change might be so that a character with a base speed of 20 (which is a hindrance on the character already) does not drop to a base of 10. That would be just too slow.
However, as you and my player mentions, this scales poorly in a linear fashion for all other base movement speeds. This is not a polymorph so you are not turning into a bear to have your base speed set to a certain number.
If they wanted to make sure that those with already slow movement are not hampered even more, they could have said "You base speed is reduced by 10 to a minimum of 20" or something like that.
Hopefully, someone from Paizo can answer this thread to let us know why they have it this way.