However, even though we call it domestic wine, anything bottled within Japan counts as domestic wine.
Literal
However, domestic wine [quot-といっても], within-country [at-で] is-bottled thing [topic-は] all domestic wine [become-となります].
しかし 'however' opens the contrastive turn. ~といっても 'even though we call it X / even saying X' is a common concessive frame for qualifying a label. 瓶詰めされる is the passive of 瓶詰めする '(to) bottle.' ~となる 'to become / to count as' is the formal equivalent of ~になる. The whole sentence explains a labeling convention — characteristic of consumer-information/industry writing.