Thank you for this, and for an overwhelming amount of references! I should say up front that I have no scholarly standing here at all; I’m a retired amateur working through a Danish translation, mostly trying to feel my way toward what’s defensible rather than arguing from any real expertise. So please take what follows as tentative groping rather than a counter-claim.
The sammā parallel struck me as a fair and important check. I don’t think I want to claim that yoniso lexically “means” causal — that does overreach, and your AN3.5 example (and the sādhukaṃ synonymy, which I hadn’t seen — thank you for pointing to SN12.62 and Ud1.1) makes we think the word itself is probably closer to a general “thoroughly/properly,” as you say.
Where I’m still uncertain is the SN46.2 case specifically. I went looking at the parallel in AN3.68, and it looks like the antidote there isn’t yoniso manasikāra directed at the same subhanimitta — it’s yoniso manasikāra directed at asubhanimitta, the opposite object (and similarly mettā cetovimutti as the antidote to dosa). If that pattern holds for SN46.2 as well, then maybe ayoniso manasikāra to subhanimitta isn’t “attending to a cause and getting the label wrong” so much as “taking the appearance of beauty at face value, staying with the surface impression,” while yoniso manasikāra involves being brought to see past that surface (whether by turning to a counter-object like asubhanimitta, or otherwise). If so, subhanimitta being causally implicated in rāga’s arising wouldn’t by itself tell us anything about whether attending to it is yoniso or ayoniso — what would matter is whether the attention stays on the surface or penetrates to how things actually stand. I’m honestly not sure this fully answers your objection, and I’d be glad to know if I’m misreading the AN3.68 pattern or over-extending it to SN46.2.
If something like that holds, I wonder whether “thoroughly/properly” and “causally-directed” aren’t so much competing translations as different levels of the same claim: yoniso as a word may carry only the general sense you describe, but in these specific contexts (āsava, hindrances, awakening factors) that thoroughness seems to cash out, in practice, as tracing something to its actual conditioned nature rather than its appearance. That would be a much narrower claim than “yoniso means causal,” and one I’m not at all sure is right — I’d value your sense of whether that distinction holds up or just smuggles the causal reading back in through a side door.
I agree with your point about ‘rational’ sounding too intellectual — even though it’s not a term I’ve used myself, your concern about overly intellectual connotations is very much part of what prompted me to start this discussion.