These all pose the same problems, correct. At the moment, I'm very unsure about how to accommodate these at all. Maybe we can have them as "custom units", which are fixed for a given property, and can not be converted.
I think the proposal to use wikidata items for the units (that is both base and derived SI as well as Imperial units/US customary units) is most sensible.
Let people use the units they need. Then write software that picks up the units that people use (after verifying common and correct use) by means of their Wikidata item ID. With successive versions of Wikidata, pick up more and more of these and make them available for conversion.
This way Wikidata will become what is needed.
I fear the discussion presently is about anticipating the needs of the next years and not allowing any data into wikidata that have not been foreseen.
There may be a way that Wikidata can have enough artifical intelligence to predict which unit prefixes are usable in common topics versus scientific topics, which units shall be used. Where Megaton is used (TNT of atomic bombs) and where "10^x ton" are preferred (shipping). And that the base unit for weight is kilogram, but for gold in a certain value range ounce may be preferred and gemstones and pearls in carat (http://en.wikipedia.org/wiki/Carat_(unit) ).
But I believe forcing Wikidata to solve that problem first and ignoring the wisdom of the users is the wrong path.
Modelling Wikidata on the feet versus meter and Fahrenheit versus Celsius problem, where US citizens have a different personal preference is misleading. The issue is much more complex.
Gregor