By all means, teach your daughter to drive manual transmission. It’s an important skill to have and not at all difficult to learn. All of my family members learned early-on how to “shift for themselves.” Now we can swap cars whenever necessary.
And the youngsters, now out on their own and buying their own cars, have each gotten good deals on used cars – chiefly because they could drive cars with manual transmissions and are happy doing so.
Whether or not you will actually buy a car with manual transmission is another point entirely, and you can decide later. I will only mention that a few dollars saved ought not to be the deciding factor. Consider the driver’s comfort level with manual shifting. Some of us still think it’s fun. The rest are far better off spending the extra bucks on auto transmission.
The Toyota Yaris is a fine little car. If that is the family choice, go for it.