1. The new version of BFO will attempt to be more flexible with respect
to modern physics (including space-time), but research into how to
represent energy and the like (and all of what you mentioned) is still
underway. Other threads have mention of wave-particle duality and the
equivalence of mass and energy.
2. BFO has: spatial region, temporal region, and spatiotemporal region in its hierarchy.
3. Unless things have changed, interpretations would not be handled by
BFO. From the perspective of the BFO, I think, they should be handled by
a lower-level ontology. Also, if the interpretation is just that--an
interpretation--and not a scientific theory explaining phenomena
existing in the world, then it would not be handled directly in the BFO
hierarchy. The information artifact ontology (IAO) may be a suitable
mid-level ontology for such entities (interpretations, theories, etc.),
or perhaps a domain-specific ontology of modern physics (and so on).
4. As far as I know there is no BFO paper on the treatment the more
exotic theoretical physical phenomena. But you may find the following
useful:
A)
http://www.ifomis.org/Research/IFOMISReports/IFOMIS%20Report%2005_2003.pdf useful.
B)
http://aaaipress.org/Papers/Symposia/Spring/2003/SS-03-03/SS03-03-006.pdf
Robert