When shin kanzen master defines the connections for some grammar forms, it often notes that である must be used for na-adjectives.
For example, in the grammar point for ~にもかかわらず in shin kanzen master grammar N2, the following connection rule is given:
名・普通形(ナ形
だ- である・名だ- である) +にもかかわらず
It seems this connection rule needs to be memorized to get the correct answer to exercises.
For example, exercise 10 on page 127 of shin kanzen master grammar N2 states:
( )の中の言葉を適当な形にして、必要なら「の」を加えて___の上に書きなさい。
...
10 この本は、内容が非常に ____ にもかかわらず、よく整理されていてわかりやすい。
(複雑な)
The solution for this exercise is 複雑である. In particular, the addition of である is necessary to satisfy the connection rule given in the grammar point's definition (as written above.)
There are many other grammar forms that require である for na-adjectives. Rather than naively memorizing all of these cases, are there general rules to know why/when である needs to be used to connect a na-adjective to a grammar form?