Disclaimer: I have an interest in neurosciece but not expertise on fMRI. I also haven't had time to read the article closely (yet). I'm sure others are better equipped to answer the question, so please jump in.
Anyway, here's my impression at a high level: neurons need energy to spike, and increased brain activity in a particular brain region ought to translate to higher metabolic activity, and ultimately to higher blood flow (to deliver e.g. oxygen). However, what one can infer about neural activity from e.g. blood oxygen level is still a matter of debate, precisely because (again as you suggested) the relevant mechanisms are complicated and AFAIK not completely understood. Other factors besides metabolism may also come into play.
Anyway, here's my impression at a high level: neurons need energy to spike, and increased brain activity in a particular brain region ought to translate to higher metabolic activity, and ultimately to higher blood flow (to deliver e.g. oxygen). However, what one can infer about neural activity from e.g. blood oxygen level is still a matter of debate, precisely because (again as you suggested) the relevant mechanisms are complicated and AFAIK not completely understood. Other factors besides metabolism may also come into play.
I suppose this article is a reasonable start:
Despite these reservations fMRI remains popular, at least in part because it is non-invasive and is one of the few tools we have for studying humans.Edit: more disclaimers. :-)