No, you should not say it-- do not tell your T "actually your face is rather plain." Talking about her beautiful soul-- and leaving it at that-- was perfect.

I can relate to your experience as well. My T has a beautiful soul and, often, when I look at her, the person she is on the inside colors the way I see her on the outside. But, truth be told, she's not exactly a looker. That, however, is something I keep to myself. I could certainly tell T "you're beautiful" and mean it- I just wouldn't clarify that it's what's on the inside I was looking at. After all, the way we "see" people is not an objective observation of the person standing before us-- rather, it is the way our eyes, language, and experience mediate what's there.