I largely agree. In it's current guise the rest system may as well not exist - but maybe they were hesitant to completely remove what has been a component of the genre forever (for better or worse).
I was kind of hoping Berath's Blessings could've been used for things like this though, something akin to XCOM's 'second wave' options.
A couple of ways you could try and make resting relevant is by firstly increasing the occurence of wounds - a 'blessing' which enables a % chance for your party to receive injuries from attacks which take out enough % of their health in one hit. It could roll against the related defense stat (deflection, reflex, fort, will) and inflict an appropriate injury. That way dumping constitution or resolve will not only make a character squishy in general but more likely to get physically injured as well.
And from the other side you could impose more of a resource penalty for resting. Significantly increase crew wages so that rest spamming away injuries or replenshing rare 'per rest' abilities and items will at least hurt your wallet. You could slow down the passage of time on the world map to compensate so you're not unfairly penalised for exploring.
Or maybe that would be terrible? It's hard to say, but I hope it gets looked at in some way or another.