1)
Not てはは but ては.
占められている: simple -te iru form
占められてはいる: connoting "is occupied by forest but there is other thing/merit than being occupied"
This は can be added into (probably) all "-te form + auxiliary verb" structures (e.g. 置いてはある, 開けてはおく, 見てはいく, 買ってはくる, etc. etc.), and an adversative conjunction such like が or けど often follows it.
2)
No. 拠点 is the object, and the location that is indicated by に is ヨンショーピング県; 多くの企業がヨンショーピング県に拠点を置いている.