The Vilna Gaon addresses this exact question. He explains that Yaakov Avinu married Rochel because of her fine character, and that she would be able to bear children that would fulfill Hashem’s wishes. Her beauty was praiseworthy because she was an “Isha Yiras Hashem”, and that is the kind of beauty that the Torah extolls–meaning her natural physical beauty was praised because she had yiras shomayim.
The gemara in Taanis also talks about how Abba Chilkya’s wife would greet him “all made up”, because it helps a husband stay focused (on his avodas Hashem). So. there is merit to physical beauty.
Beauty is praiseworthy as long within the definition of what Torah values as beauty which has many dimensions connected to each other. This is what Yaakov avinu saw in Rochel.