America's Test Kitchen did a recipe with thighs. It's was chicken
Terriyaki, though more asian than Japanese. In America chicken breasts
are the most expensive items, but in Japan it is the legs.

I think the reason people tell you to boil the marinade is in case you
want to use it to brush on to something you are bbq'ing. As long as
you're cooking at a reasonable temperature for a long time...

On the other hand, something sitting with raw meat, sugar, and water is
bound to be a breeding ground for bacteria.. especially if your fridge
isn't cold enough.