The municipal/prefectural civil unions aren't fully legally equivalent to marriage unfortunately, they do offer tangible benefits but there is still room to improve. It's not nothing, at least.

One thing I would like to note is that Takaichi doesn't necessarily get to make the decision. Japan does not have a presidential system and the PM does not have veto power. As PM she does obviously hold significant influence in the party, but the LDP is a broad tent with multiple factions, and those factions could potentially pressure her given the LDP is losing ground and opposition to same-sex rights is unpopular even with the party's supporters. Due to the constitutional law issue, I'm not optimistic about same-sex marriage in the near-term, but I do think things are trending in the correct direction, that it's likely that more legal rights will continue to be enshrined in the short-term even if full marriage recognition isn't, and that Western media creating a panic about Takaichi and Japan's supposed trend towards ultraconservatism is more oriented towards garnering engagement than accurate reporting.