it could be that coffee acts directly on the endocrine system as they suggest, or coffee allows you to work out longer (or work out at all since you don't want to sit still) which leads to the effects they observed

I'm curious why they don't mention tea actually, are they suggesting it's not the caffeine that's doing it?

granted recent studies showed decaf coffee has some benefits itself, so it could be some of the other compounds present in coffee, but a discussion of this would be useful

Decaf still has caffeine; about 30% of the original from the bean iirc.

Tea, as well as caffeine, has other compounds that are calming.

And yes, there are plenty of other compounds in coffee, as well as purely psychological effects.