@Kaartic We've had a long discussion at T152532 with this solution coming into place. The problem with a darker background is, that it is resulting in a too strong visual emphasis of the zebra lines.
We could think about increasing the vertical border-spacing a bit in order to clarify grouping a tad more:

There's also already a :hover effect on the rows as another guiding helper.

Change 435989 had a related patch set uploaded (by VolkerE; owner: VolkerE):
[mediawiki/core@master] OOUIHTMLForm: Improve HTMLCheckMatrix for further clarity

https://gerrit.wikimedia.org/r/435989

On Special:BotPasswords this results in (one row hovered)

On Special:Preferences

In T194536#4238503, @Volker_E wrote:

There's also already a :hover effect on the rows as another guiding helper.

Hovering doesn't help people who use the keyboard a lot ;-) Of course, the check box gets highlighted when :focus which might help a little but I'm not sure it helps as much as the :hover effect.

@Kaartic Yeah, I'm aware of this. It's a problematic & complex UI and we go with the best compromise here. The checkbox :focus isn't helping with the visual grouping towards the label. My patch, which just got merged is improving this with whitespace a little more.

Change 435989 merged by jenkins-bot:
[mediawiki/core@master] OOUIHTMLForm: Improve HTMLCheckMatrix for further clarity

https://gerrit.wikimedia.org/r/435989