I had a browse around. I've not been to a 'retreat' type place before although have semi-joked it may be good to go to one some time. Each to their own if this looks like a 'normal' or 'typical' one. I think in my mind when I've envisioned such a place it's more like a 5-star hotel of facilities. Perhaps where I just go hang out and read in the sunshine on a manicured lawn and get served green tea and fresh healthy meals before going for my daily massage.

Less so the compost loos. Still, each to their own. I'm more yuppie than 'hippie' (not that compost loos are necessarily hippie).
Anyway, for OP, yes your partner could have requested that he have swimwear or if she didn't feel 'right' in that and perhaps given the environment/nature of the place, then could have raised it with management afterwards. I saw they had a gay tantra workshop or something recently, so the elderly man that joined her in the tub and arrived with another man who went to shower may well have been gay. Regardless of sexual orientation, she could have addressed it somehow if she had wanted. To suggest otherwise or that you have an issue is a cop-out. Given the nature of the place though, I would also surmise she likely just went with the flow and didn't interpret any harm. Granted, didn't necessarily encourage or discourage it either. Aside from the naked part, it can't just be me thinking it would have been more considerate of naked man to at least rinse off before joining. I know, not the point..!