So, how does one reconcile this Kalachakra empowerment?
Without guru there is no empowement, and thus nothing to reconcile with.
How do we reconcile the ultimate truth and the mundane?
There is no mundane truth, just mundane lie or falsity. Tsongkhapa himself stated that so-called “mundane truths” are necessarily falsities. “Mundane truth” itself is a misnomer; the Buddha taught the two realities, not “two truths”.
Or is there even an ultimate truth?
Ultimate realities, which are the sole actual truths, can be found if you search for them; that's why they are called “realities”.
However, they cannot possibly be imagined to be what they are not; that's why they are called “truths”.
Does this mean that Buddhism is all about philosophy and less of the "supernatural"?
Buddhism is about the two realities, truths and falsities. This includes all that exists.
That all the stories of the attainments and powers of the lamas are false
Of course, because they do not exist the way they are imagined to. Which does not mean that they do not exist.
and that only the ultimate philosophy as argued by the Indian philosophers hold?
Mundane realities do hold, because they can be found if one searches for them, but they are falsities, because they do not exist the way they are imagined to.
However, some falsities no only do not exist the way they are imagined to, but also are themselves the images of what does no exist. This is the case of the evil impostor dalie and his Kalachakra imposture.
This politics in Buddhism is really tiresome.
Samsara with its images of what does not exist is tiresome. Nirvana is peace. But a bodhisattva vows never to get tired.