I'm confused: isn't this something that should be fixed per-language and, thus, something that should be done on TranslateWiki?

No, it is not fixed per language.

Sometimes, the per language approach gives a nice hit rate, since many wikis (if they have a wiki language, and if that language does not have mutiple scripts of different directionality, and if the wiki setup has not choosen something unususal, and the language used during setup happens to be the wiki language, then) language directionality 'governs' the logo placement.

Sometimes not, since otherwise, it may be not so.

Reality is more complex than the theory used to describe it, hence there are loopholes, and if you want to make it right, you have to take all the other things into consideration as well.

Thus, we may want to add an {{#LTR:yes|no}} and/or {{RTL:yes|no}} syntax to messages giving us the true directionality of the wiki at them moment. Note that it may change from one web request to another.

We could as well reword the message making it talk of "... top right corner or top left corner, depending on setup, language, and script, ..." or something the like.

My personal opinion is that we are being overly precise here. Elaborating on the peculiarities of RTL/LTR is confusing to whomever is reading it; they just expect it to work. If anything, we should simplify this message, and remove "left/right" from the message, and/or rephrase it to something like "MediaWiki's default skin includes space for a 135x160 pixel logo above the sidebar menu."[1]

Is there consensus for this?

[1] https://translatewiki.net/wiki/MediaWiki:Config-logo-help/en

Sounds good to me.

Yeah, lets make it so.
Actually, I just did it with Amirs consent.