Luxury and Taiwanese cuisine don't intersect much. Taiwan's most famous foods are typically street market fare which you'll just have to get your hands dirty for.

That said, Shin Yeh also gets my vote as far as 'table cloth'-type Taiwanese restaurants. Fortunately for your stated preferences, they have a branch on 85F of Taipei 101, which provides excellent views.

Could also consider the Aoba (Chin Yeh / Green Leaf) restaurants in this category. Possibly Ming Fu, which recently got 1*, although I've always thought it was an uppity tourist trap.

There are a lot more options as far as luxury restaurants that have a farm-to-table Taiwan ingredient focus (this is one area in which HK/SG cannot compete with Taiwan) - but those restaurants will not feature traditional Taiwanese dishes.

EDIT: as Shin Yeh at the 101 has closed, sadly. Still recommend its "terrestrial" branches.